If team A has the flag, and the last player alive on team B disconnects, then:
1. Automatically give team A the cap points, or
2. Keep the round going until team A actually caps.
Aaaand now possible issues:
1. If there's any lava in the map, the chance that the flag carrier from team A falls in it is removed. If a player from team B was about to spawn, they don't get to.
2. Could be used to run down the clock pretty easily.
Neither of those are really serious issues, though.