Well... It did burn out the deflector in "Best of both worlds".
The reason I think it should burn out the appropriate system, is that I don't want this to be a "Win button". You you could constantly re-use it, it would become a extremely overpowered skill, and people would cry Nerf... and for once I could understand them. However, this might be solved by:
[High Powered Deflector burst]
30 Common Samples
1x Rare Sample trace A
1x Rare Sample trace B
10x Aux Battery
So instead of destroying your deflector/shield/engine, you use a single item wich is consumed on use.
The idea would be, would you use this item now in the beginning of the match, to give your team the initial boost, or in the end of the match when both teams are at 14 points, and need that last one NOW to win.
Or we could you know put a long recharge on it or just ignore the minority for once when they cry nerf.