As I've noted before, the Palestinian government is very weak, and could not govern effectively if directly opposed by other factions aspiring to leadership. Such a direct confrontation could easily take place if leading militants felt that the PA had given up too much during a peace agreement with Israel. Furthermore, Hamas now forms a full-fledged domestic political rival to Fatah, and as such will hold the latter's feet to the fire on issues of corruption and management, especially at the local level.
Critics will howl at the fact a terrorist organization will be taking part in the peace process, even if their only role is comment and ratification. This is certainly understandable, and as a human I always want to see people guilty of atrocities get what they deserve. In the larger context, however, there are people in the world who have done far worse deeds than Hamas, and they walk free as dictators-in-exile or whatever whom it is simply not worth a war to punish. Nor is Israeli history entirely clean on this score, as Menachem Begin was also a terrorist. As Gandalf the Grey put it: "Many that live deserve death. And some that die deserve life. Can you give it to them? Then do not be too eager to deal out death and judgement. For even the very wise cannot see all ends"