We'd introduce Subway to them and they'd leave us be
Jokes aside though, We'd "Officially" accept the Imperium, however, there obviously would still be the hassle of religion, skitsofrenics going mad about an alien invasion, and most likely rioting on the streets.
The response from the governments would be, look what they have to offer, blah blah blah, greater good. TBH, they'd just be pressured into joining from the threat of rebellion, or annihilation, or both.
If it came to the Imperium saying, "Look, you're kind of tainted, so we'll take the non-tainted civilians along with us, and blow you up." Then all hell would break loose, people would be queuing to be taint checked by Librarians, those who are successful get to go with them. Everyone else doesn't. There'd be riots, looting, everything imaginable, and a strike at the invaders, which would mean they leave quicker.
My other scenario is similar, the Imperium gives the planet the choice of joining. If it says no then all of those who want to go with the Imperium board their ships and go along with the, the planet again goes into riot before being blown up.