To clarify, this issue has been discussed many times. Some people prefer not to have KoLmafia mess with autoattack, some get really pissed when they automatically kill such special encounter monsters without a chance to do things like re-putty. Since the former can solve their problem with one additional click, or a CCS setup for said monster such that it's never again an "issue," but the latter are pretty much borked, the devs have decided to help out the latter.
While this is one of those times where you can't please everyone, I fully support the idea of choosing behavior that fixes the problem that has no other solution, rather than fixing it for those who can still do what they want even under "undesired" behavior.