No, they aren't. They are an allegory for any immigrant group that's characterized by strong religious beliefs and customs. The things that make them resemble Muslims are (off the top of my head):
- The grags giving out the law;
- The grags wearing veils;
1 is also true of Jews, Christians and fanatics of most religions. They turn to priests for figuring out what's "true". Granted, I can't think of a parallel to Sharia law quite as harsh as the Islamist one, but the idea of separate secular and divine law is in no way exclusive to Muslims.
2 is very common. Note that Muslim priests do not wear veils, that is something done only by women. However, various religions use veils, not just Muslims:
Christian (Catholic; not quite a veil, of course, but similar to Muslim headscarves) (source)
Jewish (source; a small and obviously atypical Jewish sect)
More importantly, there are significant differences. Female dwarves are in no way subservient to the males. They simply don't wear their gender openly. That is in stark contrast to the type of Muslim you are thinking about. Even under Sharia law, women are very, very clearly recognizable as such. The religions always seemed to me to be secondary to "Dwarvishness". It's not so much a question of belief as it is a question of following "the old ways".
You could just as well posit that the Dwarves are parody of American extreme nationalism. Dwarves are trying to define how "Dwarvish" one is and whether or not they are a "true Dwarf". That's a direct parallel to the silly concept of being "unamerican".
More to the point, I think that Pratchett is using the dwarves to send up religious fanaticism, extreme nationalism and conservatism in general. I doubt he's pointing at any one group in particular. Fools of this sort are, sadly, easily found in all nations and all religions.