Nanuk,
I'm not the one you should be asking, but the end mill will most certainly give you a cleaner hole.
I've been an apprenticed mechanic and commercial carpenter, made journeyman at both and later cross trained as a millwright. Never a machinist by trade and in spite of 35+ years tinkering on guns I still won't dare call myself a gunsmith!
If you have the means at your disposal then use whats best for you. Most don't and I'm not fully equipped either even though I have a decent home shop. If I need to use endmills and Bridgeport etc, I go to my friends place!
Your sight screws shouldn't bottom out in the holes so there's no need to cut the last thread and a halfs worth. Just so long as you can drill a neat shallow hole without compromising the integrity of the barrel you're fine, no matter what approach you take. Most all gun barrels are much thicker than need be to shoot safely, so there is plenty of buffer zone to D&T so long as you are extremely careful to stay within safe limits. Naturally it depends upon the barrel in-hand to dictate what that zone will be. FWIW, a new barrel liner is thick enough in principle to handle shooting on its own. Not that any of us would try that.
I'm sure ther are others here who are able to give you a much more detailed answer than I would risk trying.
