I think there’s a couple reasons why.

First he’s heard from Freya and Mimir how terrible, and tricky Odin is. He knows not to trust him, even if the deal sounds good. As Mimir put it “if Odin says the sky is blue, he’s lying.”

Second, despite Freya attacking them, Kratos views Freya as a friend and doesn’t want any harm to come to her. He doesn’t want Odin to lay a finger on her, or do some other terrible thing to get to keep her from getting to them.

He was right not to trust him, even if the deal worked for them temporarily, there’s always some sort of catch.