Not sure if I understand your suggestion... I suppose if one wants to write server-side code in a Haskell-ish language then one would simply use standard Haskell plus Yesod or another web framework.
It is always better to have alternatives. Being self-hosting and compiling to a widely-used language like javascript is definitely a plus. Another useful case is that an interactive "Try Fay" page can be setup (like "Try CoffeeScript" page).
If the average IQ of the world population is higher, I think Haskell will become a widely-used language. Haskell is a language much more than its syntax, and takes a lot of effort to learn.
I do have some plans to make a JSON Fay-in-JS-out service. Possibly with some “export compressed as .tar.gz” feature to give you a production-ready export.
It would even be quite cool to make a REPL and development environment, but that's a little far off.