Motive: Connor has consistently freaked out the most about Sam's murder. He goes into full-on meltdown mode in the wake of the crime. Considering Rebecca threatens to turn them all in, Connor would want to act in any way to protect himself.
Evidence: There's actually not a lot of evidence to implicate Connor. There's not a notable moment where he's alone with Rebecca, he spends most of the episode preoccupied with his STD test results, and he seems pretty calm with Oliver at the end.