The Ruin storyline isn't one I've followed a great deal, but I agree that Pete seems to be the one they're throwing out there as the prime suspect, which of course automatically makes him not a suspect.
I did catch the last issue where it was shown that Luthor laid out the Clark/Superman connection to Pete and that would have made sense if that was the issue where they revealed Ruin's identity, but since they didn't I have to guess that he's definitely not Pete. The problem now though is who the heck is he? Pete from the future maybe? Young Clark Ross grown up and back through time to punish Superman for breaking his parents up? That might explain his hatred and scientific knowledge.
I'm not sure if you remember, but in pre-crisis continuity when Pete knew Superman's identity his son Jon was a major character in a few issues and also knew that Clark was Superman. Maybe they've decided to make Clark Ross a major character too.