It is impossible to do using regular JJ2. If it was possible to globally set triggers to 0 (rather than just 1, which is what crates do), you could rig up something, but it would be pretty clunky and require the base to be put inside some kind of tube system.

The only way you can have a flag carrier trigger in vanilla JJ2 is if the flag carrier is specially designated at the start of the game, and doesn't change. This is unsuitable for regular CTF, but it can be seen in some assassination levels and asbridge.j2l (an assault level).