The lady that does the SPN recaps at chron.com had an interesting idea about that in her recap here link for the epi. "In the Beginning"
She says: "I've been doing a rewatch of the show from the Pilot, and those early episodes take on a whole new meaning now..." A "...question that I was reminded of during the rewatch is why did Dean's eyes bleed in "Bloody Mary"? What's his big secret? Was it related to lingering guilt over the Shtriga? Generalized guilt for some other hunt gone wrong? Kripke has said that he knows what the secret is, but just hasn't found a way to fit it into a story. So here's my completely baseless glue huffing fanwank. Dean's secret is that he knows about Mary's deal. He knows that she's going to die, and he feels guilty that he couldn't stop it. Only, at the time of "Bloody Mary" he didn't know that he knew about the deal because he hadn't yet traveled back to 1973 in his own personal time line. Loops, dude. Loops."