As long as it's justified, no problem.
I worked for Animal Control for a while. Killed hundreds, maybe thousands of cats and almost as many dogs (including some dogs and cats I got to know and like). It's not fun at all, but if they gotta go, they gotta go.
I love animals, but they are not people. If there is a reason they need to die, I will kill them, and I won't beat myself up for it.
"A human being is primarily a bag for putting food into; the other functions and faculties may be more godlike, but in point of time they come afterwards."