Patur,
It’s not an argument defending what was done then.
The facts are we would not do today what isis is doing. Most European countries 1000 years ago committed atrocities back then, we are no different.
Until pretty recently the entire world and their legal systems committed atrocities. The main (and only) thing that matters is what we do today. If a Jewish Gadol said today that we should kill anyone who speaks against what he says or kill thieves or stone adulterers we would all agree that the Gadol that said this and his followers are out of their minds.
Being yeshiva guys we find lumdishe reasons as to why even though we wouldn’t do it today our ancestors were right for doing it then. (See Sam2 above) But that’s not really relevant.