@xris,
Good, good question; and an honest real-life one (from how it sounds).
Resolve to kill them (and find your own justification for it) or don't. I know this sounds simplistic, but I think most people simply just 'turn away' from such 'smaller' ethical issues in their day-to-day lives.
The authentic ethical life is one where your values match your behavior.
To me, animal life should be respected and cherished; but not nearly as much as human life. What I'm getting at is this: I can't kill animals indiscriminately but I will (and I have) when the reason I want them gone surpasses the amount of respect I think that life form deserves. I don't cry when I mow my grass (foilage murder) but I wouldn't take a lawn mower to a dog unless I had a really,
really good reason to do so. All things - I think - should be weighed.
If you're feeling regret for killing them;
you probably should stop (maybe find another solution). The fact that you're feeling guilt tells me its likely this might be your best solution.
Good luck.