This isn't some gangbanger who is killing other dirtbags and probably couldn't care less about Joe Schmo the Plumber...this is a person who has made it very clear that they are intentionally in the business of killing and maiming civilians.
People were justifiably worried that this person posed a serious threat to their own safety and while having your house searched is certainly stressful, it beats walking out on your lawn and finding an improvised explosive sitting there with your name on it.
I get the "police state" angle, but based upon the spontaneous reaction Law Enforcement received in Watertown after the capture, I'm going to hazard a guess and say that they were pretty understanding of what happened at their own expense.