Yes, you are correct. The Bible is specific about who God wants the Israelites to eliminate and there was a valid rationale for it. Because the Israelites did not wipe those people out, they had to deal with wars with them for centuries until the Assyrians captured Israel and after them the Babylonians. At some point the Philistines vanished as a civilization. Historians do not know what happened to them. They probably got tired of constantly fighting with people all around the Mediterranean and they just assimilated into the local cultures.
With Islam the command is to kill all of the infidel in perpetuity. Allah was only specific with "the people of the book" meaning Jews and Christians. "The book" is the Bible. In one place Allah commands Muslims to either tax or murder Jews or Christians. Then that commandment was superseded with kill all the Jews. In addition kill anyone who will not convert. So basically kill everyone.
That commandment was never rescinded and in case you haven't noticed, Muslims have been killing people who will not convert. They'll kill other Muslims who they think are not Muslim enough.
Jews and Christians are not like that. Yes there was the inquisition but the inquisition wasn't the Catholic Church just sending people to kill heretics. The inquisition was started to give people who were convicted of a crime under the civil courts a second chance with an ecumenical trial. Sometimes the inquisition would save the person from capital punishment. But if the person was actually guilty, the inquisition did not execute the person, the civil courts did.
However, I think over time the inquisition probably got drunk with power and very much overstepped their bounds.
Still the number of people who died either by the civil courts or later on the corrupt inquisitioners was far less than the number of Europeans killed by Muslim invaders all through out the middle ages and into the Renaissance. In fact Barbary Pirates (Muslims) were attacking our merchant marines when ever our trade ships entered the Mediterranean Sea. This was becoming so frequent that the merchant marines started wearing leather straps around their necks so that the Muslims would have a hard time beheading them. This is why our Marine Corps are called "Leathernecks" to this day.
So there is a massive difference between what the God told the Israelites and what Allah tells the Muslims. You don't see Jews running around trying to kill anyone