Your post is not very clear to me: are you staying in Jordan with your wife or are you abroad?
I am not sure but if a Jordanian woman is married to a foreigner he cant ask for a Jordanian passport after some time.
Although I heard a couple of years ago that this law will changed, but then again, I am not sure. On a second thought, you can apply for a permanent residence but this is different then for applying a passport,
The best you can do, or she, is to contact the Ministry of Interior Affairs. I posted a link on the sticky thread: "Great links for newbies" on the main forum.
If this is all not possible then you have to renew your passport at your Embassy and asking every time the visa.