I think that counterargument #2 would generally be compelling. Most religions have flexible dogma that changes with the whims of society, and even in those that don’t the actual practice of that religion does. Unlike Thudlow Boink, I really think the comparison to biological evolution can be useful-- if a religion really is firm in dogma and practice, it can’t respond to changes in the “environment” of society and it dies out as it ceases to appeal to people in that society. This is part of why religion is so much stronger in the US than in most European countries-- those countries had established state religions that had static dogma enforced by the state, whereas religions compete on a ruthless survival-of-the-fittest playing field in the US. We can barely go 50 years without a Great Awakening! So, to get to the OP, I think we should generally blame those atrocities on the society at the time, since the religions that provided the excuse for them were mere reflections of that society and bear little resemblance to how those religions are practiced today. (I think you could make an argument for religion in general helping those atrocities by providing the excuse, but it’s harder to say that something unique to the core tenents caused them).
The only trouble is that most religions deny the above. So while I don’t think we can really hold them accountable for those atrocities, if they’re going to claim that they have an unchangeable and infallible dogma dating back to or past those atrocities, I think we have every right to do some serious eye-rolling in their direction.
Also, this isn’t really how biological evolution works either. The idea of “more evolved” and “less evolved” organisims fell by the wayside a long time ago-- you could maybe make a distinction between more complex vs. simpler species, but selection pressures can cause them to “evolve” in either direction. There is no end goal towards which organisms (or religions) are evolving.