You may want to specify down on a certain conflict or far more specific time frame than this. "Age of musket" is a, frankly, horrible term and it lumps together over 300 years of history which experienced arguably the greatest change in Western warfare ever. It's absolutely impossible and even more irresponsible to lump civilian deaths of the Thirty Years' War, the War of Spanish Succession, the First Coalition War, and the Peninsular Wars and just "average out" their civilian casualty rate or to compare army pillaging and looting practices across this entire frame. Just doing one moderately sized state like, say, Brandenburg-Prussia and later Prussia and analyzing the practice of looting and pillaging they performed or even had performed against them would be 2-3 beefed up posts for "the age of musket".

/u/elos makes a valid point, the "age of the musket" is a pretty vague period, which really spans across 2-3 (or more) different periods common in the study of military history. Edit: and by the length of this post, you can tell how big a question this really is. I would call this a general answer.

But to present a very general answer, there are two major periods concerning the treatment of civilians by armies and martial authorities. That is the period preceding the Thirty Years War (1618-1648), and that following the War.

Before the Thirty Years War, civilians were treated as they always had been: that is to say poorly. Wherever an army went, they tended to desolate the country side. In extreme cases, this was the result of strategic policy, where a general would employ scorched earth tactics against the people of whomevers countryside he was currently marching. In these cases, licence was given to loot, murder, pillage, and indulge in all the worst aspects of humanity. But even if a general showed "restraint" in his dealings, that rarely mattered for the individual "civilian". Most armies, well into the 17th century, were very poorly supplied. Money, munitions, and all the daily necessities rarely arrived from the home country. Vast distances, theft, corruption, wastage, and all sorts of factors generally reduced pay and food to a trickle, if it got through at all. This forced soldiers to forage for food. But these men rarely strolled through the forest picking berries and hunting deer. The armies had to move to fast for that, and besides they had sharp pointy things which would aid them in just taking whatever they needed from the populace. This was extremely bad for most armies, as it sabotaged morall and local support, but it was critical to the success of a campaign. And while the soldiers took food and drink, they often took anything of value as well. And, regardless of the general's personal feelings on theft, pillage, and rape, it was often seen by the soldiers as their just compensation for waging war. After all, money rarely flowed from home.

However, the Thirty Years War changed that. It did so, because it was one of the biggest and nastiest wars ever fought in central Europe. Some historians have argued that it was the most destructive conflict to ravage Germany before the World Wars. Thats really hard to quantify, and exact statistics are woefully lacking. But suffice to say, the actual fighting of the Thirty Years War both directly and indirectly devastated Germany. Not only for the reasons listed above, but also armies spread plague, and they slaughtered the rural population, and even whole cities, based on their personal religion (protestant vs. catholic). As armies fought and refought over land, they horror that they brought slowly forced peasants out of the countryside and into cities, where disease took a massive toll. And with most fields unplanted, and the remaining food confiscated for use by the Army, starvation and famine were rampant. Finally, the largely mercenary armies which fought the war were absolutely brutal. They were encouraged to kill, rape, and steal from members of the opposition group, and they were allowed to indulge their most horrid desires on a regular basis. This made their behaviour even worse, and its possible that out of control soldiers started sacking several cities on their own volition. So the Thirty Years War was pretty brutal, and in many ways it was the ultimate extension of the concept of "total war" before the advent of industrialized warfare.

Following the Thirty Years War, wars became more "civil" concerning their treatment of noncombatants. While no formal codification existed until the 19th century, armies slowly shifted away from ideological wars which mandated the complete annihilation of the enemy (purge the heretic), and switched to more limited wars. By the dawn of the 18th century, pillaging was the exception, not the norm. Several examples, notably Louis XIV's pillaging of the Rhenish Palatinate and the Duke of Marlboro's pillaging of Bavaria were traumatic moments. But an important distinction is to be made: they turned their armies lose on the regions, the armies didnt do this themselves. And this largely happened because the conduct of wars changed. Between the 1640s and the 1690s, logistically, armies switched to what is called the "magazine" system. Essentially, instead of living off the land, troops instead lived on the end of various supply lines which originate from several "magazines". These were huge, well built fortresses which contained most of the implements of waging war, including weapons, and they also allowed generals to pre-position food for use during campaigning. The system itself was desirable for a number of reasons, but generally the lack of pillage made armies tamer, and more easy to control. Men who pillaged left the watchful eye of their officers, and did as they pleased. But under the magazine system, men were forced to always obey their officer's commands. But the system also radically affect the way wars were fought. Rather then fight for cities and great swaths of territory, armies were tethered to their magazines, supplies were slow to arrive, and limited the speed of any potential offensives. Further, a magazine was a vast fortified base filled with potential for an enemy counter-offensive. They had to be taken out, lest they pose a threat to your own supply lines and rear. The upshot of all of this was that wars were relegated to more narrow areas, and sieges were (largely) conducted over strategic fortress, rather than large population centers.

This really remained true until the Napoleonic period, which again released the specter of ideological warfare. But actually the Napoleonic period was more "friendly" to civilians than the preceding Thirty Years period. It wasnt until World War One, that armies again became barbaric. But by that point, weve probably left the period youre talking about.

One last thing to mention in all this, is how small a point were talking about here. Large armies maybe occupied the space of several miles, and the most disorganized bands of mercenaries would likely loot an area of the map smaller than the tip of a pin. They were not the armies were used to today, which form massive cordons that sweep across continents. These forces were limited in their size and reach by simple magnitude. 100,000 men and their equipment dont take up that much space. What really affected the civilian population was constant warfare. In a few weeks or months, armies could only devastate a smaller area. The number of people that were affected was thus low. But over 5, 10, 30 years, of constant conflict, those areas became huge. Places never had time to recover, cities (centers of trade, governance, and population) were irrevocably destroyed, and people were displaced in huge numbers. This all started a domino effect. As some regions stopped producing food for years on end, they displaced people and dismantled the early markets of the region. As entire regions fell into disorder, those disfunction markets affected even larger regional and continental markets, which themselves further exacerbated the suffering of those in war torn areas. And as they suffered, the repeated the cycle, thus ensuring chaos for years to come.