There are many implementations of EDSLs which take the approach that you want to take by using Haskell to create a syntax tree and the offshore it to some backend compiler. None of them uses a timeout. The difference is that they implement all the transformations after the parsing phase, and there are no Haskell functions or arbitrary data types in the syntax tree (unless we bring generics into the picture).
But in case you really insist on a timeout I would recommend using a wrapper function on the toplevel of your metaprogram which implements the timeout. That way you don't have to risk your sanity by having to dig around in GHC. Of course, as soon as I give everything an explicit representation, this part of the story is straightforward.
Gergely -- http://www.fastmail.fm - Accessible with your email software or over the web