I hear ya brother! I have had itchy allergy eyes my entire life and unfortunately I have rubbed my eyes with pepper soaked fingers.
No fun, and it could actually cause permanent physical impairment if not treated properly.
Immediately rinse your eyes with cold water and take that dreaded trip to the emergency room.
You can save yourself a lot of pain and aggravation by using gloves while disecting your peppers.
Good luck all,
Bill