You can apply the flagcapendsround to flags and/or bases. This makes it more customizeable, since you may want to make the one-flag mode end on a flag cap, but not with 2-flags.
As for "getting rid" of things, hm -- perhaps I could just make them instantly respawn. I think the way it's set up, entities are never actually removed or created, just relocated (while that could be changed, I don't feel like doing massive restructuring of the code -- usually means lots of bugs pop up).
Hm, yeah -- trigger once's should be reset (or maybe a new entity created in case you want to really have something only triggered once ever).