I'm probably going to regret starting this without the aid of a diagram.......
If I'm reading this right, you just want to reduce the slack - tension of the tow line when bouncing over waves? Bungee will stretch a certain percentage of it's overall length for a given load, so, if you have a long bungee tied (say) halfway along your towrope, for a given extension of it you'll need less force to extend it, therfore reducing the load on the a- frame. Alternatively you could tie it to another bridle at transom level, which will reduce the bending load.
The fun bit ids going to be setting it up so that it takes enough slack up without ripping the frame off the transom....... Could also add a short length of thick- ish bungee to the tow line itself to prevent "snaps"? (although if you get that wrong, it could be amusing to watch!