OK, I'm having a REALLY hard time seeing how making beams free by default would break backward compatability.
I thought that it was FRED that had the beams locked by default, NOT the game. In other words, I don't think that the FS2 exe has anything to do with beamfree, but that the FRED exe has everything to do with it.
For example, a mission has its beams locked by default (because nobody freed them in FRED 2.0, the beamlocked version). You change to FRED 2.1 (beams FREED version), but the missions themselves don't change. Thus, the game reads them the same way, and the beams that were locked before, stay locked, and vice versa.
I hope I'm making sense...
But I think the best way to go about it would be to have a "beam enabled" toggle box next to each beam cannon in the initial status display. If you want to enable or disable any of them later, use SEXPS.
It's like the sabotage SEXP. You don't use it when you want a ship to start out damaged, you use the initial status display.
Wait, I just had a brain wave. In addition to (or instead of) a check box for the beamfrees, have an entry box to enter a time delay, just in case you want this ship to me emerging from subspace sometime in the game.
Just a few thought by lil ol' me:-P