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Based on reports from multiple people, the Jordan land-border crossings with Israel WILL stamp your entry visa/stamp onto a piece of paper if asked. They will not do this by default, but if you ask them to then they will most likely do so - however there is technically no guarantee they will do so, so as always it's a good idea to ask nicely!
If you are doing a tour that returns back to Israel then you should be fine with simply getting this visa stamped on a piece of paper. However if you were planning to depart Jordan via air then it's important to be aware that the immigration staff at Queen Alia International Airport (and potentially other airports) will generally NOT stamp your exit stamp on a piece of paper even when asked, and even if your entry stamp was on a piece of paper.
This leaves you in a situation where you have an Jordanian exit stamp but no entry stamp in your passport - which can also be a sign to other countries that you entered Jordan overland from Israel.