I am not sure about Dubai regulations but if you want to be on the safe side you'll need to do 2 things:
1.Ask the Jordanian passport control not to stamp your passport.
2.Ask the Israeli passport control not to stamp your passport.
it's important to make sure the passport is not stamped in the Jordanian side because if its got stamp there it means only one thing - that you visited Israel (even if your passport was not being stamped in the Israeli side).
I think it will be wise to ask Dubai authorities what are the regulations regarding foreign passports with Israeli stamps. I guess that after the assassination of Mahmud Al Mabhuh things have been changed there because they hold Israel responsible for that (you might ask this also in the Dubai forum).
There is no problem visiting Israel via Jordan from Dubai. I recently ran across a group from Dubai in the north of Israel (less than a month ago) who were foreign nationals. Although I don't know if their passports were stamped, I do agree with Elad that you check with the Dubai authorities along with the Phillipine authorities to see what needs to be done to assure re-entry into Dubai without problems.
Keep in mind that while Israel has an official policy and procedure for not stamping your passport - according to what others have posted here in the past, the Jordanian authorities do not have such a procedure. They will stamp your passport and then it really doesn't make a difference if it is stamped in Israel because it will be obvious that if you left Jordan at a land crossing to Israel you had only one way to go.
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