didn't you read, notice that his sempai sexually harassed him, almost raped him and twice?!?! any person in his right mind would react the same way good grief. his sempai broke and betrayed their work relationship bonds. Naoya did more, he prevented Tsukasa from beating the perv sempai and any situation that would create problems for the company and also kept his work relationship with him when he shouldn't.
how to say it... i think this is not a bad story, but i don't really like the uke. his senpai helps him a lots at work, even if it's for personal reasons, but still. and then when the uke received his confession, he acted like his senpai is some kind of freak homo, and even avoids him like... avoids some perverted :p