I think the point is that you're not supposed to know. Chris has to trust tony's word and even if he doesn't tony said the guy has to go so he has to go regardless of the reason.

The guy may have killed chris' dad, maybe he didn't, it didn't matter. Maybe Tony as geniunely doing chris a solid by giving him vengence or maybe he was manipulating chris. In that world you more often than not don't know anything for sure and just have to go by what you're told.

I think that was the point of that scene. The audience doesn't have all the information and doesn't know and it ultimately doesn't matter because that's how it is in that life.