K.C.
We did a Disney cruise in the Caribbean last fall with our kids (then 5 and almost 2). My husband and I did a European (Western Mediterranean) cruise before we had kids, so I can give you some advice on both.
First of all, DO IT!!! I cannot begin to tell you how much we enjoyed both vacations and how much I would LOVE to do a Disney cruise in Europe. My son (the older one) had so much on the cruise that he still - 8 months later - repeatedly asks to go back. He talks about the kids club, the water slides, and the other fun activities on board. He had a blast!
My son is allergic to dairy, eggs and all nuts - we avoid them all 100%. We had absolutely no problems at all on the cruise. Our waiter for our normal dinner even personally brought up room service for my son one night to ensure that his meal was correct. We ate breakfast at the buffet every single day and never had a problem, we also frequently had lunch at the buffet. They will cook things specially for you whenever needed. They will have your son order his dinner the day before so they can guarantee that it is prepared correctly.
What ports is it going to? There are so many amazing tours and things you can do. My favorites were Rome (Civitavecchia), Naples (and Pompeii), Athens and Santorini. Others were all great as well, but those were my favorites. In Rome and Naples, we booked all day tours through private companies whose primary business is cruise ship tourism, so they totally understand the need to get back in time, they pick you up at the boat, etc.
Disboards.com is the best place to go for all things related to Disney Cruises. CruiseCritic.com is the best place to go to find out about things to do at the different ports. On both sites, you can join a group specifically for your sailing.
I am so jealous... totally wish I could do this cruise!