I think you just do what you can and recognize that there are things you can't do. That doesn't mean that you pretend it isn't happening, but you acknowledge that you can't be a perfect preserver of all life in every single second. You can try to avoid harming things while knowing that you won't always succeed, and while understanding that sometimes you need to act even when it does cause harm, and just try to minimize it. You're probably going to crush a lot of microscopic stuff, you may even crush quite a few small insects from time to time, but you can keep something of an eye out and not do it intentionally without a good reason.

The best you can do is exercise the empathy that you're able to, try to encourage others to do the same, and let go of the parts you can't really control. You can think of it like hygiene on an outward level. Take a shower, wash your hands, brush your teeth, change your clothes, but are you going to throw your shoes away every time they touch dirt? Are you going to wash your hands every time you touch a surface? Take dozens of showers per day every time you sweat the tiniest bit? Wash your clothes again and again before even wearing them because the air itself isn't perfectly sterile? Hopefully not.

Do your best, but exercise moderation.