Dan,

I had a thought. What if there was a racial building that had a chance to negate artifact effects? Make it for one of the unlockable races like the zolazin. Size one has a 15-25% (idk what exactly is fair) chance to negate any harmful artifacts used on a planet.

I'm still working on other ideas for the various races. EG. Konqul racial building that adds 1% of planet population as tactical officers or helmsmen to your crew. It'd reduce the planets pop by that much and transfer them to your ship.