I don't know about military force "alone", but terrorist groups have been defeated through primarily military means. Generally though, military force is a rare solution. The RAND corporation did a pretty indepth study of how terrorist groups "end", and concluded that military force was rarely the best option; with only 7% of the groups they studied being defeated primarily by military force. However, when the terrorist groups become strong enough to conduct insurgencies, military force ups to about a 25% success rate for ending terrorist groups.

http://www.rand.org/pubs/monographs/MG741-1.html

The bottom third or so of the report has a table that lists individual terrorist groups and shows what circumstances led to their end.

In his book, Violent Politics, former Ambassador William Polk argues that military force is about 5% of the formula to defeating terrorists. The other 95% is undermining both their political power and their infrastructure; in other words, taking away their ability to recruit (by making them unattractive to join) and dismantling their ability to wage war (by removing financing or weapons shipments, for example). Purely military means rarely works as /u/houinator explains, and I can find no example of any violent group (insurgent, rebel, or terrorist) which was defeated through military means alone; most commanders and strategists use multi-tiered attacks upon their targets. Even the Romans when battling piracy in the Mediterranean mixed naval campaign with denying pirates ports.

Source: William Polk Violent Politics: A History of Insurgency, Terrorism, and Guerrilla Warfare from the American Insurgency to Iraq Harper Perennial, New York, 2008.

It might be worth pointing out that unfortunately, many interesting answers to this question would fall within the last 20 years, and the sub uses a 20 year rule to draw a line between historical and current discussion.

As with any discussion about terrorism, we ought to start out by defining what terrorism is. There are an inordinate amount of definitions of what terrorism is (even among the various American government agencies, there are varying definitions), but the common theme among all of them is that is the politically motivated use or threat of violence by (generally) non-state actors against non-combatants.

As this is /r/AskHistorians, let's examine who some of the first terrorist organizations were. Generally regarded as the first "terrorist" organization were the Sicarii, a fanatical splinter group of Jewish Zealots active in the first century CE in what is now modern day Israel. Seeking to push Rome out of the promised land, they would stab to death Romans and Roman sympathizers in broad daylight. These actions escalated hostilities between the Romans and the Jews, and eventually culminated in the First Jewish-Roman War. In their last stand at the Masada fort, the Sicarri succumbed to the overwhelming Roman army, and most of them committed suicide. So in this instance, military might alone did defeat terrorism.

The Assassins were another proto-terrorist group that operated in Persia during the 12th and 13th centuries. In case you didn't figure it out by now, they are where we get the word "assassin" from. The Assassins were notorious for assassinating political figures in public. They were wiped out by the Mongols by the end of the 13th century. So in that instance as well, military might alone defeated terrorism.

Now back in those days, world leaders tended to be much more liberal with their use of force against political threats. These days, most terrorist organizations are able to avoid complete decimation because they know that their demise will also mean a lot of collateral damage toward the civilian population, which most nations (with the arguable exception of nations like Russia and yes, the United States) do not want on their hands. So it is rare that terrorist groups are ever defeated through force these days.

So now we must differentiate the various types of terrorist groups. On one hand you have your religiously-motivated groups like al-Qaeda, ISIS and Aum Shunrikyo. On the other hand you have separatist groups like the Irish Republican Army, the Palestinian Liberation Organization and the Basque ETA. You have your ethnocentric terrorist groups like the KKK. You also have your lone wolf terrorists like Timothy McVeigh and the Unabomber. More recently we have seen the emergence of narcoterrorist groups—typically Mexican and South American drug cartels—who have no real political ideology other than a bloodthirsty lust for wealth and will use whatever political influence possible to achieve that end.

To be clear, there is some overlap among all of these. ISIS could arguably be categorized as a separatist group due to their territorial claims, and the IRA/PLO could also be identified as having religious motivations as well.

But the point is that how these groups end really depends on their types. Separatist groups tend to fare the best as they are the most open to negotiation. In the case of the PLO, the IRA and the ETA, they all reached some sort of consequential end that caused the majority of their members to either give up violence or splinter off to form a new group (e.g., Hamas).

In regard to religiously motivated groups: Because governments tend to be cautious when it comes to quelling this types of terrorist groups, what often happens is that these groups continue to exist but sort of fade into irrelevance. While politicians say they will "crush" or "defeat" terrorist groups, what they really mean is they will contain the threat that they pose. We have arguably contained the threat that al Qaeda once posed in terms of domestic attacks, but since this is /r/askhistorians, we won't really know for a long time how everything that is going on right now will play out. Of course, the threat that ISIS poses could be greater than what its godfather group posed.

So in modern history, it isn't too common to see terrorist groups defeated through military might alone—though ironically, the threat of military force can hasten their demise. It's not really a joke to say that most terrorists tend to burn out on it after awhile (when I have more time, I'll dig up a study I remember reading that found that most terrorists quit their groups after being in them for a good number of years). Most modern terrorists tend to be underemployed, middle class, though decently educated men in their 20s. By the time they reach their 30s and 40s—assuming they haven't been killed yet—they just decide it's not worth it anymore, and their groups just fizzle out.

Lastly, as someone who studied terrorism as the primary focus of my undergraduate political science degree, my very humble opinion is that some incarnation of groups like al-Qaeda and ISIS will always continue to exist so long as the Middle East remains a vastly unequal resource-rich, opportunity-poor, feverishly religious region. That's not to say military force is ineffective in reducing the threat that terrorism poses. But in this day and age, you do tend to need more than just missiles to defeat ideas. That is all just my own speculation, so take it with a grain of salt. Only time will tell.

Sources:

• What Terrorists Want. Louise Richardson. 2006.

Coincidentally, there is the case of the Kharijites

This fanatical sect initially arose during the first Islamic Civil War period, where the camps of Ali and Muwaiya were at each others throats. They basically were the first hardline, extreme Islamism advocators who basically took the stance that none but God could rule over Muslims, and they rejected both Caliphal (?) candidates. This movement dispatched 3 assassins to kill 3 key political leaders in this time: Muwaiya (military governor of Syria, founder of the Umayyad dynasty), Amr ibn al'Aas (military governor of Egypt), and Ali (cousin/son in law of Prophet, 4th Rashidun Khalifah, source of Shia-Sunni split). They were to be conducted simultaneously. First 2 failed, last one found Ali in the Grand Mosque of Kufa. Killed him with a poisoned blade while he was prostrating. Those assassins were found and killed as per Islamic law, and the movement petered out.

The Kharijites would resurface 2 centuries later under the Abbasids and sow a rebellion, again with more or less the same rhetoric. This was met with full military response over the course of rule of several Caliphs. There was no discourse, there was no push for compromise, there were no concessions entertained. The only acceptable solution was military extermination, and thats exactly what happened. Though it took a while, thats exactly what was done and the movement was stamped out for good...or so it would seem.

I think this is a fitting example for many reasons. Even though this is ancient history, the Kharijites not only fit the description of modern day terrorists to a tee, i.e non-state politically motivated violent actor with minimal public support, they were dealt with by violent military force: because quite frankly thats the only language they spoke.

On a less academic note, there is a popular sentiment in modern Islamic discourse that groups like ISIS and AQ are modern day incarnations of these same Kharijites. This doesn't really add anything to the discussion, but I do find the symbolism and parallels to be quite interesting..

Certainly. Montoneros in Argentina and Tupamaros in Uruguay, just to mention my corner of the world.

http://en.wikipedia.org/wiki/Sri_Lankan_Civil_War

Sri Lanka, being an Island, made things easier.