There are a few other good products that have no whole corn, but do contain small amounts of corn-based distillers grains. I don't know if those would trigger your horse's allergy. My horses both get "skin funk" on corn, but small amounts of very processed corn (like in distillers grains) don't seem to bother them.
Don't fall for a girl who fell for a horse just to be number two in her world... ~EFO
If allergies are a concern, often your best bet is to go with single ingredients and mix your own. Beet pulp, oats, alfalfa, rice bran, etc. can all be purchased in individual bags and you can make your own blend depending on what the animal needs nutritionally.
agree with deltawave - making your own is a great way to know exactly what your horse is getting. if you have a local feed mill, you could perhaps have them mix up something special for your horse's nutrition requirements?