If a real war played out the way the simulation did, and the Hashemites were killed and lost Jordan, then even if Arafat didn't want to take Jordan his people would take it without him. I don't see how he could restrain his people from leaving the west bank and heading towards Jordan. They would perceive it as a friendlier place to live then on the west bank.
Since they would have control of Jordan, but still be in hostilities with Israel, natural laws would dictate that, like water, the people will move along the path of least resistence. With heavy resitence on the west bank and none in Jordan, it wouldn't take very long before the west bank emptied itself of Palestinians.
That is NOT the way things happen in the Middle East - or anywhere else for that matter. Some people of ALL groups choose the path of least resistance. Many do not.
It was not the path of least resistance that lead Israelis to the settlements. Some Palestinians may indeed leave. But the task of much "cleansing" will remain to be done.
The one body not mentioned in the wargame is the UN. Their "refugee camps" would still be extant and those who have lived in them without working for five generations would go on living and being supported there. The problem would persist.