There is no official or even apparent problem for you to enter Israel.
Jordanian passport holders can ( and do ) enter Israel without a problem.
The only thing that might happen ( do to other factors like Name / Appearance ) is that you will be held for short questioning ( like I have on multiple occasions for various reasons ) to check other factors underlying your visit ( for example - relatives in Israel / Palestinian territories, reason for entering etc ).
Be sure to give the right and honest answers and don't panic. The young people holding these "interviews" are usually firm but nice and if there is really no other problematic reason or factor - you will be on your way in one minute.
The Jordanian origins or passport by themselves are not a factor.
On a side note - I see many questions in here regarding similar fears of having Arab / Muslim origins travelling to Israel and although I can understand the premise - people tend to forget that there is a large population of Muslims Arabs in Israel that live there, work there, have an Israeli citizenship and passport and the local security / authorities are no strangers to Arab / Muslims - and in fact many of them can even speak the Arab language to some extent.