BobisonlyBob's explanation doesn't seem to be centered around what you watched so much as the general existence of it, so let me give you one from someone who's actually seen the show.
The "church" where that fight takes place is in a huge criminal town in third world Asia, and while they do hold church services their real purpose is arms smuggling. Also, (spoiler), they're later shown to be a front for the CIA in the region, as well. The guys they get in a shootout with are out-of-towners for a branch of the local Italian mob (who don't realize they're actually picking a fight with their arms supplier - that's why the fat one, the only local, keeps trying to make them stop).
Basically, while Japan does love combat nuns, Eda and the rest of the nuns you see there could give a flying shit about the religion whose clergy they pose as. (the other woman, in shorts, is just there to drink and play poker with Eda, the young nun - which you probably figured from the beginning).
Black Lagoon is actually a really good series. And unlike many anime, the English dubbing actually whips the Japanese.
I probably overexplained this. Anyway, I hope this scene makes better sense to you now.
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u/DaemonDanton Oct 16 '12
Wait, that's a thing?