After seeing CotT, I honestly dont think it will have a bearing on Thor whatsover. Sure there are God's in it, and Zues of them even wields lightning as a weapon but the whole Thor/Clash of the Titans thing is like apples and oranges. The God's in CofT arent even seen that much, and are seen using their powers even less [with the exception of Hades], then there's the difference in tone and approach to factor in, not to mention the world of difference in terms of the filmakers' calibre.
I mean, c'mon, does anyone think that CofT left that much of a lasting impression on moviegoers that it would hamper a movie coming out over a year later?
I know I dont.