There's a lot wrong here, so I'll just highlight some terms and quotations from this this essay that strike that strike me as being used in an anachronistic or analytically flawed way with some comments in italics:

• The inventor of insurgency warfare - let's get a big fat "citation needed" here
• Muhammad’s intelligence service - 'service' implies a structuralized bureaucracy. The "shurta" as an elite stability-maintaining police force has been ascribed as evidence of the existence of security-based state institutions, but I am unaware of any such "intelligence service"
• In his thinking and application of force Muhammad was a combination of Karl von Clause­witz and Niccolo Machiavelli, for he always employed force in the service of political goals. - Clausewitz, to my reading, suggests that ALL war is used in such a way, so this strikes me as a truism.
• grand strategist - *There are debates about attributing things like "grand strategy" to peoples who had no such doctrines, but I guess I'm ok with it.
• a fiery religious guerrilla leader who created and led the first genuine national insurgency in antiquity that is comprehensible in modern terms - Citation needed. 'national' in this context is anachronistic.
• guerrilla cadre - really?
• national military force - again, not national.
• Insurgencies also require a messianic ideology - Do they?
• a messianic replacement for the clans and tribes that were the basis of traditional Arab society. Islam certainly up-ended traditional Arab society, but clans and tribes were hardly replaced.
• Muhammad chose Medina as his base of operations because of its strategic location. - Muhammad didn't choose Medina so much as Medina chose him.
• It is essential to understand that the attraction of the Islamic ideology more than anything else produced the manpower that permitted Muhammad’s small revolutionary cadre to evolve into a conventional armed force capable of large-scale engagements. - *I would tentatively agree with this but I suspect for very different reasons than the author is getting at. Islam created a framework in which the previously fractious Arabian tribes could unite, but the army was not "Islamic" per se, containing as it did many non-Muslims.
• At the Battle of Badr (624 ce), Muhammad could only put 314 men in the field. Two years later at Second Badr, 1,500 Muslims took the field. By the 628 battle at Kheibar, the Muslim army had grown to 2,000 combatants. When Muhammad mounted his assault on Mecca (630) he did so with 10,000 men. And at the Battle of Hunayn a few months later the army numbered 12,000 men. Some sources record that Muhammad’s expedition to Tabuk later the same year was composed of 30,000 men and 10,000 cavalry, but this is probably an exaggeration. What is evident from the figures, however, is that his insurgency grew very quickly in terms of its ability to recruit military manpower. - While the idea that Muhammad's armies grew must be true, any kind of reliability of these figures down to single figures given the source material is preposterous.
• a secret police that could be called upon at a moment’s notice to carry out whatever task Muhammad set for them, including assassination and terror. - Citation needed.
• Abbas served as an agent-in-place for more than a decade - I mean, ok, that seems to be gilding the lily a bit.
• We have no knowledge of exactly how the intelligence service was organized or where it was located. That it was part of the suffah, however, seems a reasonable guess. - Ah, ok, so you're guessing.
• He used terrorism in two basic ways - *There's no standard definition of terrorism per se, but I'm disinclined to use it in the way the author is using. The use of terror and the terrorizing of populations, including with mass civilian slaughter, is not the same thing as 'terrorism.' The Mongols understood the strategic value of terror, but were not 'terrorists.'
• against a Jewish tribe of Medina, he ordered all the tribe’s adult males, some nine hundred, beheaded in the city square, the women and children sold into slavery, and their property distributed among his Muslim followers. - *Whether this actually happened is a matter of significant dispute. Had he done it we might expect such behavior to have become a typical Islamic practice based on emulation of the prophet. It did not. The source of the story, IIRC is from Tabari a couple hundred years after Muhammad's death whose source was a member of the tribe in question.
• The old Arab way of war would have had no chance of success against the armies of either of those empires. - That the Arabs were actually deeply familiar with those ways of war, having been clients of their neighbors for centuries, is generally thought to be pretty important, so I don't think it's their 'way of war' so much as the scale of forces that was possible under the new regime.

I could go on, but the structure of the essay seems to carry on with equally exhausting and tenuous assertions and back-readings of history.

All of this is without getting into the biggest issues which is that our ability to reliably say anything specific about the prophet's life is a matter of significant historical doubt.

For why that is, I would suggest reading Robert Hoyland's essay Writing the Biography of the Prophet Muhammad.

For better histories of the conquests and early conquest state I would suggest either Hoyland's In God's Path, or Fred Donner's Muhammad and the Believers, or both.