As a matter of fact our batei din were never bloodthirsty the way ISIS is. Executions were extremely rare. But that is beside the point. The main difference between us and ISIS (and us and the Nazis and every other bad group that ever lived) is that we were right and they are are/were wrong.
Meaning, there is no objective, outsider, point-of-view that can be used to examine the actions and positions of any group from a moral perspective. Our morals and values are shaped by the society we are brought up and reside in. Very little, if anything, can be said to be objectively bad.
Klal Yisroel received a direct transmission from the Creator of the Universe as to what our morality should be in many different situations. The same Creator that revealed that infanticide, in general, was wrong, also said that in the special circumstance of the shiva umos, it was required.
We, and modern society that was influenced by us, find the killing of children to be so repellant specifically because we have imbued the value of the sanctification of life into society as a whole. I do believe that the mitzvos are meant to achieve that effect on us, making violence against the innocent repugnant to us.