For me, it’s not even about the idea of Lucasfilm disregarding comic/novel canon or other armchair Story Group concerns - I just feel like the change actually takes away from Kanan’s overall backstory. While the broad strokes lead him to the same-ish place, his trauma and pain almost feel less earned than it had been?
We never got a concrete exploration of it in Rebels ofc, but even without the comic, the situation is talked as heartbreaking primarily for specific thematic reasons. The comics only provided an explicit version of those events that dominantly interpreted the ideas Rebels alluded to: Caleb finally feels at home (they had just won the battle), secure in his place in the galaxy - with his master and his close friendship with clones like Grey and Styles. That being when the rug is pulled out from under him is undeniably as tragic as it is confusing, and breaks his trust for a long time.
Not that the situation isn’t inherently sad in Bad Batch, but the sudden confusion of it all is the dominant emotion. Which makes sense for the perspective of the Bad Batch, but the tangible adjustments made to the sequence (time, setting, players involved) do no favors for Kanan’s character. He’s now accompanied by clones he just met that day - who don’t even end up really wanting to hurt him, one of them even letting him get away, and he knows it. It’s just such an odd sequence that leaves mixed themes.
I don’t typically mind retcons at all, truly; the Ahsoka planet/saber stuff from S7 or the lekku stuff from Mando was silly controversy to me, but this one feels off because it’s not even a better change, and it would have been easy for it to not have been Caleb.