I'm a strong atheist but Buddhism has always been the religion I've respected the most. At least the philosophical aspect of it.
I used to struggle with this too. To this day I use a box to pick up spiders or mosquitoes and take then outside instead of killing them. But I wouldn't doubt killing termites to save my plants.
We kill everyday. When we walk, or drive the car. We're powerful giants. But we can be respectful giants.
It doesn't absolve us from our "sins", but it's far better than nothing.
I think it can be narrowed down to "be respectful". Letting your rats die would be disrespectful to them. Killing a spider that isn't harming you is disrespectful to them. Walking on top of ants you know are there is disrespectful to them.
[1] http://venyifa.blogspot.com/2008/09/story-of-compassionate-s...
“The strings break,” the musician replied.
“And what happens when you string it too loosely?”
“When it’s too loose, no sound comes out,” the musician answered. “The string that produces a tuneful sound is not too tight and not too loose.”
“That,” said the Buddha, “is how to practice: not too tight and not too loose.”