I think it might be feasible for raid starships perhaps(since there will be so few of them--they could update targets much faster--might be too much work on the backend to handle something like this though). I agree that computationally its not feasible for parasites now that I consider that aspect of it.
Heck, even giving raids something simple like a damage boost when enemies are below 1/2 or 1/3 hp might be cool?
Another idea would be for parasites to have an instakill chance(and perhaps very very low base damage(1?)), but base the instakill chance on the current hps of the enemy(so its very low against high hp enemies, but higher as the enemy gets lower--say equal to (1/the number of hits from that parasite would be needed to kill an enemy with the current system)--Then they do the same expected damage to enemies, but are more likely to end up with kills, In a sense all of their damage will turn into conversions...) also makes more sense in the case that you kill a ship, and it instantly comes back with 1/2 health?--rather have it "instadie" (or rather switch sides), and have some fraction of the health it had when it was forced to swap.
Edit: this would cause parasites to be more useful out of supply(as the enemies they kill will generally have more hp), but will cause them to convert less than the current system(since they will basically have high burst damage but lowish dps).