Why would it be harder for a Palestinian state to harbour terrorists than it is for the Palestinian Authority?
Iran, Syria, and Lebanon are all examples of nations who harbour terrorists with impunity. (Syria is even on the UN Security Council.) On the other hand, it will be harder for Israel to fight terrorism when the territories are sovereign. Besides, as Dov Anashlowich constantly points out, the Palestinians can always make demands later, and by legitimizing terrorist acts, people like you are making it more likely that they will ask to redress their grievences through terrorism.