Thor would be a formidable opponent, but the God of Thunder is not incomparable to many of those Kratos has already destroyed. After all, what chance does Thor really stand against Kratos, a God who is likely even more powerful than the God of Thunder, if the likes of Zeus could not?
Thor and Kratos fighting would undoubtedly be explosive and devastating. Just look at his track record when it comes to battling gods. He has annihilated Titans and Olympians alike, while also demonstrating that he can compete with Norse gods such as Baldur. Although it has not always been easy, he has always found a way to defeat his adversaries.
Few gods have the raw strength and power of these two, so any clash between them will be memorable. Picking a winner is difficult, but Kratos would most likely win in the end.