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As far as I have heard it is not a problem if you have a stamp from Israel, all they are worried about is people with an Israeli passport.
If you haven't already seen this, the following is all that it says on the Malaysian Immigration website:
No visa is required for U.S.A. citizens visiting Malaysia for social, business or academic purposes (except for employment). No visa is required for a stay of less than one month for nationals of all ASEAN countries except Myanmar. For a stay exceeding one month a visa will be required, except for nationals Brunei and Singapore. For national of Israel, visas are required and permission must be granted from Ministry of Internal Security. For national of Republic of Serbia and Republic of Montenegro, visas are required and permission must be granted from Ministry Of Home Affairs. Nationals of countries other than those stated above (with the exception of Israel) are allowed to enter Malaysia without a visa for a visit not exceeding one month.
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