Well, Doctor Octopus killed Tarantula and Kaine, and Scorpion is currently in SHIELD custody (and has the tail permanently welded to his body, so its definitely not him).
If it is a clone, it's a clone that genuinely believes that he's Peter and not someone trying to screw with the cast, given his opening monologue to himself in the first issue.
I'm 99% sure that the Peter in the comics at the moment is the genuine deal.