You know when you jump into a bot sector, and you do a little *pew pew* and the message comes up when you clear the sector of bots?
"Great Work! You have cleared the sector of bots!"

There should be some kind of reward for doing this.
I recommend a faction bonus in whose space it is.
Lets say +10 faction standing.
If you like, too, give 500+ Combat?

I think it will make players more attracted to fighting the hive for their nation.

-Estrian Prosis

This only makes sense.

I think you do get a reward of some sort, don't you?

No, just the message. It might be incrementing some hidden counter, but nothing that is obvious to the player.