Here's another way to look at this situation:

What if this happened on the flop. Minimum bet is 100. BB checks. UTG raises to 300. Neither MP nor CO raise (it doesn't actually matter if they fold or call). BB puts in 100. What's the ruling?

Presumably, someone would tell BB that the bet is actually 300. But, if BB had never said "call" or "raise" when he put out the T100 chip, would you allow BB to raise? If not, how is that different from the pre-flop situation?

Obviously, if he said "call," but only put out T100, you wouldn't allow BB to raise. Isn't that what happened here? His check was actually a call in the wrong amount.