Hi Carmie,
I left your query for a couple of days to let someone who has done this trip respond.
I'm going with JY to Jordan in April. I can understand where your concerns are coming from but I personally are not concerned in the slightest.
In this region of the world Jordan is held to be one of the most stable countries. You see on the news them taking in people from Syria but we will not be anywhere close to the areas affected. I am also led to believe the people are most welcoming and with tourism taking a hit, they are only too glad to see you.
Recent reviews on Jordan on the forum say this is a wonderful trip - don't miss out if that's where you want to go.
Hope this helps.
Angie