It depends if the eye-fi card is an X2 version (which I suspect yours will be if it's new). The older non-X2 cards are reported to work fine with ML, but the X2s don't set boot flags so if the camera's nvram is expecting to boot from SD (after installing ML using a normal card) it simply won't start. You can't even get the Canon firmware to load properly, you need to uninstall ML before swapping to the eye-fi card then re-install it afterwards (not only is that a pain, it raises the question of how many times we can safely rewrite nvram).
See http://www.flickr.com/groups/magiclanternfirmware/discuss/72157627990119618/#comment72157627879367185
I don't see much hope for fixing X2s in the short term as eye-fi would have to change their products (it may be fixable by a firmware update to the eye-fi card itself, but there's no commercial argument for doing so, given how few of their customers want to run ML). People have asked them and gotten nowhere.
See http://www.flickr.com/groups/magiclanternfirmware/discuss/72157627990119618/#comment72157627879367185
I don't see much hope for fixing X2s in the short term as eye-fi would have to change their products (it may be fixable by a firmware update to the eye-fi card itself, but there's no commercial argument for doing so, given how few of their customers want to run ML). People have asked them and gotten nowhere.