There is a good book on this kind of thing: Franzen, Godel's Theorem: An Incomplete Guide to Its Use and Abuse. There are lots of different reasons why Godel's theorem is not relevant to the search for a TOE:
Physics is not axiomatic system.
We don't have a TOE, so we don't know whether Godel's theorem would apply to it, even assuming that it could be made into an axiomatic system. Godel's theorem only applies to certain types of axiomatic systems. For example, it does not apply to elementary Euclidean geometry, which can be proved to be consistent.
It is possible to prove that one axiomatic system is equiconsistent with another, meaning that one is self-consistent if and only if the other is. If we had a TOE, and we could make it into an axiomatic system, and it was the type of axiomatic system to which Godel's theorem applies, then it would probably be equiconsistent with some other well known system, such as some formulation of real analysis. Any doubt about the self-consistency of the TOE would then be equivalent to doubt about the self-consistency of real analysis -- but nobody believes that real analysis lacks self-consistency.
Finally, there is no good reason to care whether a TOE can't be proved to be self-consistent, because there are other worries that are far bigger. The TOE could be self-consistent, but someone could do an experiment that would prove it was wrong.