I think where stability is concerned, each tick would could as one projectile hit, which would work fine in beam vs. projectile cases.
You're right, though, for beam vs. beam things would need to change, but not necessarily for the worse. Thinking about it now, each time a beam would lose a projectile, it could shorten a little until one is pushed all the way back to the shooter. Adds some good old fashioned beam on beam battling, I'm thinking like DBZ. It shouldn't be too complex to calculate the beam tick rate and stability stat to determine which beam pushes the other back and at what rate. I think increasing the size of the projectile also affects projectiles canceling each other out, which probably wouldn't be too difficult to figure out and balance and would be pretty cool.