Um.... It depends on which Link. Link from the 2-D Zelda games? Hell no. Link from Wind Waker, about 50/50. Link from Twilight Princess and Link from OoT? He would wreck Kratos's shit.
As for the "Kratos has killed gods" theroy, he has killed Greek gods. We must take into account the fact thta Greek Gods can be killed, whereas other deities are different. No one can kill the Christian God, as their religion says so. We must assume that, since this is a crossover, the rules from both universes apply. Link could also kill the Greek gods (in theroy) because their laws allow it to be so. The gods of Hyrule, however, cannot be killed. Therefore, Kratos couldn't kill a Hylian god.
We also seem to be forgetting that, if Link had access to the Triforce, he would be granted any wish he wanted. This includes Kratos's death.
We must also consider the fact that Link was chosen specifically by the Gods. He is the "Chosen One", if you will.
Also, the reappearing of him in every Zelda game is proof that, if killed, he would simply reincarnate in 100 years or so.