1. At that point the spirit is a cornered animal, it's self-defense to go after Dean no matter what he's done in his past.
2. Dean's the type of guy to blame himself for deaths even if they weren't his fault.
3. When Dean failed let the Shtriga get to Sam and failed to kill it while it was feeding on Sam, which in turn caused the distraction of John driving them to Pastor Jim's giving time for the Shtriga to escape, all those kids the Shtriga was sucking dry probably died - and Dean probably blames himself for that just as much as he blames himself for letting Sam get hurt.
So, to me, Dean's eyes' bleeding was a non-issue. Then, last night I was reading the Supernatural Companion to Season 1, and came across this quote from Kripke: "There is something in his past - we've always known it. It's been in the core of the character from the time we created him. We will reveal it...."
Damn it! The thing is: I'm sure Kripke has forgotten. Dean has gone and done way worse things since then - torturing people in hell and enjoying it, breaking the first seal...there's no way they're going to do an episode where some secret from his youth is revealed, because at this point Sam (and us) will just be like "Oh, 's'at all? Whatever."
So, I really don't think we'll ever know what Kripke intended, because I'm pretty sure he doesn't intend it anymore. I could be wrong, but I doubt I am.
I much preferred my version of why Dean's eyes bled...instead of Kripke telling us he actually did intend something...because now I'm all curious as to what it was he originally intended.