Dont know, it would make it more unique than the average "Jason kills a bunch of teenagers having unprotected sex" thing.
Maybe he left Pamela because she was well... crazy even back then, maybe he was ashamed when Jason was born due to his apperance so he ran or maybe he didnt even knew she was pregnant at all. Maybe he just found out what happened since then and wants to help/stop his son.
It would be interesting how Jason would react to it, he loves his family... well his mom anyway. Unlike Freddy or Michael Myers who don't care about their parents and would kill them without remorse(I dont count Rob's remake), Jason is the only one who was always shown capable of loving. It would put the character in a situation we never seen before, we dont even know if Jason know what a father is.
I doubt his mom ever explained how having a kid works, she probally teached that sex was evil but she never went so far, even the concept of a father is unknown to him. If his father started to explain who he is and his relation with Pamela, Jason would probally freeze without knowing how to process the information.