It seems that this decision was very deliberate by those that pushed for it and those that agreed it. Rather than trying to come to agreement with the PA over these sites, the intention was to bypass the PA, assert Israeli authority and control over West Bank sites, and humiliate Palestinians and their leaders. It worked very well.
Sinai bomb attack could have targeted peacekeepers, official says (AP)
from the article: Israel and Palestinians pass the Jericho test