If I remember correctly (I try not to use Steam if I can avoid it) you can install/uninstall games from Steam whenever you like. I am not sure how many times you can do that (there must be some limitation for obvious reasons).
Regarding GWX there is no uninstall routine. If you don't want GWX then you have to manually delete the entire thing.
My suggestion if you want to use SH3 from Steam is to make an extra copy of the SH3 folder and then install GWX on the copy. That way if you want to get rid of the mod you still have the original SH3.
If you need more help just give us a shout
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