After finding out that Caitlin logged into his computer, he goes to extreme measures to make sure it's destroyed. Clearly he has something to hide.
Taylor finds out that Jeremy was secretly stalking Nolan when he was alive.
After Taylor shoots Jeremy, it is revealed that he has been secretly working with the professor this whole time. Perhaps he is the one who did the dirty work?
Why He's Not the Killer:
Based on what the professor says about the experiment, it seems like Jeremy is a small piece in a much bigger puzzle.