These are interesting questions, but I think that a practical line gets drawn for us: you simply can't avoid killing something that you can't see. Sure, in certain cases you know that you might be killing some microscopic organisms, but there really is no point in worrying about that, because you kill microorganisms involuntarily all day, every day. Even your body is killing things at this very moment.
I think my sig is relevant here: there's a difference between doing what you can (not eating meat, etc.) and involuntarily killing something you can't see or avoid. We can only do so much... being veg*n is enough, I think.