radiation wears off, takes an age, just leave a colony ship parked next to the asteriod with autocast colonise.

By the time you have Novalith, tax income should make up less than a fifth of your total wealth, so it's really not a big deal unless it strikes a fully-populated terran (your homeworld, for instance).  The radiation clears after like 8 minutes and the planet will be habitable again.  Typically you don't fire the Novalith at planets you are about to capture, instead focusing on planets that are behind enemy lines.