Biggest Piece of Evidence: Ezra is clearly managing a lot of anger right now, and he also seems miffed about Charlotte's release. Plus, we know he met up with Aria the night Charlotte died, and we don't know what he did once they went their separate ways. The nail in the coffin is Spencer's criminology paper, which is frighteningly close in detail to the circumstances of Charlotte's death. Ezra read that paper.
The Point of Contention: Maybe the fact that he's so consumed by his grief is a sure sign he's too distracted to murder Charlotte. He has his own problems to worry about.