Suppose you were living several thousand years ago in a village in the Near East. Put yourself in that context.
You receive word from a messenger that a nearby village has recently been destroyed by another tribe who claims that they were told by their god that they are chosen people. The tribe is on their way and were told by their god that they must "totally destroy all that belongs to you". Furthermore they were told by their god to "not spare you; put to death your men and women, children and infants, cattle and sheep, camels and donkeys." The messenger also says that these people say that anyone who believes in a different god must not be spared, should be put to the sword and killed.
Now suppose, you are living today in Syria. Put yourself in that context. Suppose you hear the same thing about a group called ISIS.
Same region of the world. Different time. If you could time travel back and forth between the two time periods, is there any method that you, as an external observer, could use to ascertain that the God of the Israelites should be worshipped while the God of the Muslims should be fought against?
Note 1: Remember to picture this from the perspective of an ancient Near Easterner. You do not yet have the hindsight view of post-New Testament interpretations. In the same way, today we do not have the potential hindsight view of ISIS in the year 3000 A.D.
Note 2: For reference I am looking at 1 Samuel 15, Deuteronomy 13, and Numbers 31 with regards to Christian beliefs and Quran 2:191, Quran 9:123, Quran 9:5, among others with regards to the beliefs of Muslim extremists (e.g. ISIS).
You have captured a portion of the nature of the battles Moses, Joshua, and the Jews fought when gaining the promise land.
The canaanites worshiped different gods and sacrificed their children to these gods. But as long as we are doing an epistemic experiment lets focus on what warrant the Jews might have:
Seeing the Red Sea parted
Seeing God put a pillar of smoke by day and pillar of fire by night in their camp
Seeing God destroy the Egyptian army
Delivering them miraculously with 10 plagues prophesied
etc.
We are talking about a culture that had seen enormous justification for believing their God. And we should examine the truth-claims of Islam seriously. Not brush them off as violent and abhorrent. The truth of Judaism, Christianity, and Islam don't stand or fall based on their bad actors (ad hominem fallacy) but rather based on their ability to best account for the world we encounter.
It is obvious that once we find out in the future the truth about religious claims, the majority of claims will turn out to be false.
But also in science, when we finally figure out the grand unified theory it will be on the backs of tens of thousands of false theories that appeared inductively true at some point in history.
So limits to knowledge shouldn't scare us. We have rationality, and can examine claims.
Finally, if the Judeo-Christian God is the true God, then he has the right to judge his creation as he sees fit, being the creator, being all-knowing, he would not only know everyone's past intentions, and the damage they caused, but also future damage. Being the standard for justice he would know whether the punishment fit the crime.
So any attempt to analogize the destruction of the Canaanites with ISIS terrorism would be nothing more than an appeal to emotion.
Finally, there is a lot more going on than just a divine command to grab land, it is related to the giant clans in the north and ties to 1st Enoch. But that is a rabbit trail for another time.