Pick and chuck, lol! No, really, unless you're willing to work with them and work through things, you really can't do much with them. I'm not aware of any device that would keep you from having to touch them, other than a rat trap and that would largely defeat the purpose since you asked about pregnant females. Gloves, maybe, although they can be hard to hold at times.

Some of mine are "meaner" than others, including the one that bit the snot out of my finger which is still bearing a Band-Aid as I type this, lol! They're like anything, they all have personalities and some are "nicer" than others. I've worked with most of mine, either prior to them being pregnant or while they're young, getting them used to being handled and some are to the point they actually seem to enjoy it. Best advice I could offer is jump in with both hands, expect to be nipped if you have a mom with a litter and most of all, don't be afraid of them! Wash your hands before you handle them so you don't smell like food, be mindful of the moms with litters and as to the males, well...they generally could care less about much of anything besides a female in heat and/or food/sleeping, usually in about that order when it comes to mine!

Is your issue with them carrying germs/disease or something else? The disease/germ factor by and large comes back to you: keep them in sanitary conditions and you won't have any issues. If you can smell the bin (urine, feces), other than the "warm animal smell", it's way past time to clean. Practice good husbandry for them and for yourself: wash your hands before and after you handle them and don't touch your face, eat, etc. prior to cleaning up. I don't know if that answers your question(s) or not; hope so and I hope it helps. Good luck and take care!