I think you can probably set the flags for the it much more nicely via
http://hackage.haskell.org/packages/archive/Cabal/1.16.0.3/doc/html/Distribution-Simple-Program.html and the haddockProgram record.
heres an example Setup.hs that does something very, similar, in this case making sure that "-pgmc clang" is passed to ghc always.
that should help!
I hope that helps! :)
(while you're at it, adding the -pgmc clang thing from my example setup.hs would probably prevent the funny build errors I was hitting, :) )