Dr. D? It would indeed be cool, but its almost the definition of overpowered. Maybe if the arcs just do HE damage so shields could block it...
True, you'd want shields to block it otherwise...rather OP. Though you can do some other things to balance it, such as having a two minute warm up time, by which time half the fight is already over anyway. On top of that your other ships are probably already engaging them in close ship to ship battle basically meaning you're going to be sacrificing them/doing damage to them.
Another thing you could do...is have it if the weapon or ship is hit with EMP damage whilst charging the weapon, it overloads - setting the blast off prematurely inside your ship (ouch!).
But my word, would it be awesome to wipe out a screen of enemies and your own with the Little Doctor.
"Oh noes! It's a fighter swarm!"
"Ska-dooosh" the ultimate anti-fighter weapon.