At least for now, I have made Piercing Thrust and Shocking Spear only hit enemies, but raised their SP costs by 10 to compensate. For comparison:
Ghost Bite: Range 2, 70 Power Pierce, hits one target but can hit any square in range without line of fire. 15 SP.
Piercing Thrust: Range 2, 70 Power Pierce, hits one or two targets but only if they are enemies. 20 SP.
Shocking Spear: Range 2, 85 Power Pierce/Elec, 10% shock chance, hits one or two targets but only if they are enemies. 25 SP.
In effect, Piercing Thrust costs more than Ghost Bite because it's basically Ghost Bite that can also hit 2 targets at once if they're both enemies. If all you really want is attacking through allies, Ghost Bite is the better ability. Piercing Thrust can do that too now, as well as hit 2 enemies when possible, but you pay SP for that versatility each use.
More direct beam attack adjustments might happen later, but I still have nightmares of the last time I messed with that code.