The key entry is the 0 internal damage for the Alloy Burner missile. However I neglected to make it skip shields, which is why the damage amount was lower than you'd expect. Anyway, the idea was that a temporal ship might employ Shield Accelerators and ABMs to remove shields/armor quickly. Although thinking about it, not sure what advantage removing armor might convey...
Plague Warheads are a good idea, but it might be too effective. Plague Bombs on Drones don't suck though - they're only 20kT and fire every 2 seconds, so a small group of plague drones could still plague a planet even with heavy PD. That's a reasonable compromise given the nastiness of a plague.