I put my mice in hot water for about 10 minutes. I have to change the hot water out about 3 times, but the mice end up nice and warm.
You want to minimize the amount of time the mice are above 40 degrees, and feeding in a separate container probably helps with any lingering bacteria.
Overall, though, our culture has made us germaphobic. Your snakes don't need to live in a sterile environment- in fact, that would be bad for their immune systems.
That is the reason the CDC recommends against using antibacterial hand soap- it is bad for the human immune system.
I use white vinegar diluted half with water for the vast majority of my snake cleaning. Vinegar is non-toxic and an antibacterial agent/ deodorizer. Using harsher cleansers is a risk to your snakes.
Snakes should never be allowed to crawl through their excrement, as that can cause infection. That is why an absorbent substrate is good to use. I remove poop at least once a week. Water bowls should be taken out and cleaned regularly. A full tank clean should be done about every 3 months.
Remember that moisture leads to bacteria, so keep the moisture down. Humid hides should be temporary and kept fairly sanitary.
Those are my sanitation tips.