There are definitely tiers to experience. I would expect that a rat can suffer far more significantly than a mite, or even a thousand mites.

Beyond that, your rat depends on you as a pet. I’m afraid that, if you can’t adequately look after your pets because of your beliefs, then you shouldn’t have pets.

The way I learned is that you try not to meddle unless you have wisdom (meaning you have some kind of enlightenment). My opinion is that unless I was the one tormenting other beings, I wouldn't meddle in other person's affairs, specially by killing. This is a good example on the importance of finding a teacher, a Good Knowing Advisor, someone that can dispel these doubts for you.

There's the obvious self-defense exceptions, if a lion or a person would attack me or my family I would shoot him, but an enlightened being may act differently because they may understand something we don't.

Any system of beliefs is going to have a few internal inconsistencies. Speaking from cheerful ignorance of what Buddhists actually believe, from my understanding the "don't kill things" is something in the nature of really good advice grafted on top of a philosophy that really an acknowledgement of impermanence and a set of guidelines around how to live with that. There is no sustainable belief system that stops its people from becoming soldiers.

If everything dies, at some level killing isn't such a sin. There are real practical populations if people use that as a serious philosophical starting point though.