1) Fortress good align is held to a different standard as non-Fortress good align. It's against the principles of the cabal. Battle? Doesn't care so much about you killing other goodies, but your align in general is still at risk.

2) Bad luck? Sure. "Acceptable ####-up?" The whole idea of this is as a good align, particularly in Fortress, you shouldn't accept "acceptable" screw-up.

Goodie invoker blows up a city block to kill Istendil.

Looks around at the three random citizens nearby.

"My. That's unfortunate. Those guys shoulda gone elsewhere."

...

Uh...no. The invoker should be having severe issues with the fact that he's now just as murderous as whatever bad-dude he's fought.

Obviously it's not my playground, but I think that's the biggest issue going on. We've gotten too used to treating NPCs as objects in the game, and this has been a bit of a shift moving away from that. Amusingly, a number of years ago my last Fortress dude got promoted from Scribe to Acolyte *because* I was running for my life from some evil dude, passed the plague along to an NPC, and ran back to heal the NPC.