My husband is a beekeeper, and I am not, so take this with a grain of salt. I wouldn't worry about killing a bee here or there. It just happens. Watch out for queenie, but everybee else is part of a larger organism, the colony.
If you are a beekeeper you will and probably should get stung on a semi-regular basis. If you don't get stung, you'll be exposed to the bee venom in small amounts while never getting a full "dose," and this could lead to an anaphylactic reaction when you finally do get stung. IDK if this is theoretical or proven, but there is a very high incidence of bee allergies among beekeepers' families, but not the beekeepers themselves. DH actually does his bee laundry (anything he wears out to work hives) separately as a precaution. I have not been stung in the 5-6 years he's been keeping bees. I probably should. Also, we have a friend who has been keeping bees for years and years, and recently had an anaphylactic reaction. This beekeeper always wore a full suit and never got stung. It could be a coincidence, but I think not. Also, beekeepers are particularly long lived as a profession. So it's probably good for you to get stung for living forever purposes.
You need to do a fling test or some other test to make sure your honey is totally "cured." IDK if that is the right word for it or not, but you don't want to take nectar off the hive that hasn't completely become honey yet, because the moisture content could be too high and the honey could ferment.
If you are extracting the honey with a machine, my guess is you go ahead and cut the comb top off, and bees will hang out with the cut stuff while you extract from the frame. If you are doing crush and strain, just go ahead and do your thing, ignoring the bees. They'll probably hang out with the comb and honey above whatever you are using to filter the honey. Ignore them and bottle it up.
Anyway, those are my thoughts as a beekeeper observer. Hope they help somewhat. Also, there are other forums out there just about beekeeping...