I had always been one to ask for alterations of menu items to fit my vegetarian/pescetarian needs, but it took going out to dinner with vegans (no disrespect to vegans, you guys are doing a great thing!) to realize how frankly annoying and disrespectful it is when you walk into a restaurant and ask to change everything the chef put so much work into perfecting. Don't worry, I'm guilty of doing it too, but if you want to completely customize a dish you're better off staying at home and cooking it on your own. If you have an extreme allergy, by all means ask for alterations to prevent an epi-pen epidemic. If it's a matter of moral issues or taste preference, just make it easier for everyone and try for a restaurant that has at least a couple dishes that cater to your dietary needs.
Seeing both sides, it's hard to find a stance to take. Do you stand your ground and avoid meat completely for political or emotional reasons or do you avoid being offensive? One one hand you don't want to support the meat industry or find it completely feasible to sustain a healthy life without animal products. On the other hand, sometimes you just have to look at food from another emotional and artistic perspective: someone put their heart and soul into that chicken soup, so you better suck it up.