What if
Brian left the bar (undetected). Clint knew he was going home or might have told him to go home (he was seen shortly, talking to Brian). After Clint and Meredith leave the bar, Clint goes to Brians apartment, confronts him somehow, there is a struggle, Brian is dead. He takes Brian to a different location and gets rid of the body. Then, in the morning, he returns to the apartment, stays there for a few hours (to clean up and make things look as normal as it can be). To the question why he was in the apartment, he could have simply answered that he waited there for Brian.
Note:
-we dont know how Clint got keys to Brians apartment
-we dont know if Clint had an alibi