My idea for how to get the Handicap CTF concept working originally was something like this:

Every base is in a tube. Once a player goes through that tube, he grabs the flag and hits a crate, with ID 0 for example. Him hitting the crate closes the base. He also touches a trigger zone.

When the flag bearer of a team is killed, he dies, and he (somehow) hits the crate that opens the bases again..so that the other flag bearer can score. When scoring, the flag bearer hits a crate that adds the handicap, and opens all bases again.

And then Blur reminded me that teams are supposed to be able to regain the flag after they die. And also it's sort of late and I'm confused with my original idea. So ignore this.