No reason at all for anyone just to remove the bike without attempting to locate the owner. I'd make a formal complaint to the manager over that one. If taking bikes indoors is prohibited and there's no sign to say as much then perhaps suggest the employee is lucky you're not filing theft charges with the police. You could also point out to the manager that if the employee had damaged your bike you'd have held the store responsible, and give him an idea of what sort of costs might be involved.

Personally I don't like leaving my bike out of sight at all. Last time I went to the bank in town I picked up my bike and walked right on in with it, and nobody bat an eyelid. Smaller shops and more crowded shops might (understandably) not wanting people bringing things in that just block the way for everyone else, but that's still no excuse to just pick up your bike and take it away.

I have been known to call ahead and ask if a store will let me take my bike inside, with the usual implied rider that if they won't then I'll give my business to somewhere that will. Locking the bike up a couple of blocks away and then having to take off the lights, GPS, pump, bottle, saddle bag etc etc etc just seems like too much hassle.