Then I suggest the use of particles to make it seem like there's an energy barrier there. You can still shoot through it, but not jump through it.

That's actually how it's done in this map..
Although it's a tad buggy, though, due to the teledest sometimes teleporting the player into the room above the scoring method room, which has an alternate scoring method where both attacker and defender flag are stacked on top of eachother (thus causing rapid scoring).. I'll fix this and introduce some balance changes in an upcoming update. :)

I've been considering making an assault-style map for a while now, and how to make the scoring work was a problem for me too...
The most recent method I've come up with is this: Start the attacking team off with the opponent's flag and give them a goal. At the goal, there's a teleporter which teleports them to a small room, containing (from top to bottom) the teledest, their flag, and some death (the material). That way, when they go in, they score and then they die. The dying is necessary so the defending team can't go in, grab the flag, get back out and score when they're defending. Works pretty effectively (at least in my head).

Of course, that's designed for a one-way assault, where both teams have access to the goal, but...

Yeah, it would be nice to see an improved version of this map :o)