When he does it, he screams "You call yourself soldiers? Cowards!" or something to that effect (it's in the same episode). So he thought it was evacuating soldiers. Also, in Destiny, it's in a flashback when Yzak says that "I should have died a long time ago" (so it was portrayed as a sin of his which he regretted). And as I said before he might be a pissy guy but he isn't a bad guy or in any way evil.

But yeah, it's too bad. As I said before I'd like him more if he actually knew he killed that little kid off. I hate overly cute anime kids.