In The Orlando area there is Whole Foods and an independent natural retailer of the same scale called Chamberlains. I think a new whole foods opened up in the Sea World area, near international drive. Also, Publix (a grocery chain) has a fairly decent health foods section, especially in the more affluent areas. I'm sure there's at least one in Windemere, near Disney, that will have a good selection.
Raw milk is only legal as pet milk. There is a guy who brings it into Orlando from farms to the north, but only every-other week on a very specific day and the pick up is no where near Disney. You have to sign up with him -- way more hassle than you need on vacation.
Cocoa beach is the closest beach, but depending on when you're going (like if it's later than October), you might be better off heading out towards Tampa and the warmer waters of the Gulf. Also I believe there are fewer rip currents on the gulf side than around Cocoa Beach. Cocoa Beach is one of the worst areas for rip currents in the country (well, from Daytona down to Cocoa beach is). The zoo in Melbourne (near Cocoa Beach) is MUCH better than the one in the Orlando area, and really about the same distance from the Disney area.
Totally go to the keys if you can, it's fabulous there! Definitely more a small town like place. I doubt there's a whole foods, more likely small local health food stores. Key West is nice, but it gets really crowded with tour ships coming through. I like it for a day trip from other keys myself. If you are headed to the keys, you might consider stopping on the way from Disney in some place like Sanibel Island. That would also be a GREAT beach location, lovely in the fall, and about 4 or so hours from Disney, perfect for breaking up a drive to the keys!!