Well, I think it WAS Jonathan. I don't think any other male would affect Clark that way.
As far as Christopher goes, I have to admit (drags feet, here)it is nice that Clark is admitting the possiblity that Christopher could be his, biologically.
As far as refering to Christopher as "his" though, I still don't see it as a big deal. He acts like Chistopher's dad, Christopher calls him "Dada", and he loves him like his son. Doesn't that fit the definition of a father? Once again, I will remind you that Jonathan is not Clark's biological father in canon or this story. Would anyone think it was werid for Jonathan to call Clark his son?
The kiss was nice, I admit that to.