In FMP, these weapons also had two tiers and they were simple increments in power: first the weaker version, then the stronger one. It was okay, but kinda dull.
I could drop these from MiBs, but... they also use all sorts of other weapons you shouldn't know at the point where you protect D. Vincent: lasers, blasters, plasma, alien grenades... I realize they don't have their paths as complex as the gauss tree, with retroengineering and all, but I feel we would have to address them as well.
The best I can do is to ensure make captured Mass Drivers researchable so at least you could use them. But I need to move VERY carefully here, because the branches of this tree are quite prone to breaking.