If you have a serious allergy, then that is clearly a “special situation” where bending the rules of etiquette is acceptable. If bringing your own food to a restaurant is what you require, than you can do so. Of course, whipping out a Tupperware and chowing down isn’t okay. But the last thing a restaurant wants to do is cause you illness or worse, and they should be glad to accomodate you, if you approach the situation correctly.
Here’s what I would suggest.
While your party is being seated, ask to speak to the restaurant manager. Speak to him/her out of earshot of other patrons if possible. Probably the most important thing is to take an apologetic tone. Explain that you have “very serious food allergies,” and that you unfortunately can’t risk eating food that you haven’t prepared yourself. Bring a disposable plastic container with a dish that doesn’t require heating or anything. It should be something that can just be put onto a plate. Ask if it would be possible to have the meal plated and brought out with the rest of the entrees. Say that you’ll be happy to pay a “plating fee” if necessary.
Assuming the manager isn’t a moron, he will gladly honor your request. He doesn’t want to hurt you (not because he’s such a nice guy, but because lawsuits suck) and will appreciate the fact that you have arranged it so that it won’t be obvious to the other patrons that you are eating food that you brought. Also, he knows damn well that his prep area isn’t clean and that there is a ton of cross-contamination going on. That’s just how it goes in restaurant kitchens.
You do not have to tell him what your allergy is. The fact that you have a serious one is all the information that he needs. If he protests that they can accomodate any allergy, then be extra-apologetic, and tell him that you have learned the hard way that you have to be this cautious.
And if you get a bad vibe from the manager, go ahead and eat from your disposable container. Apologize to your dining companions and waiter, say you have a very serious food allergy, and don’t feel one bit bad about it.