Theodore hadn't expected the Professor to get up just to let him in, but although he saw that Snape was busy as he entered he didn't ask if he should maybe come back later; he didn't see why his favourite teacher would have asked him to come in had he been busy, had he wanted Theo to come back later.
"I'm sorry to disturb you sir-" Manners were a different animal. "- but I received this by anonymous owl and I thought it was best I bring it to you before I opened it."
It might have been a paranoia that a lot of his classmates wouldn't have understood, but Theo wouldn't have thought to do anything else on receipt of such a thing.