Well if you have an autoimmune disease and your doctors are telling you stay away from milk/dairy, you probably should! So what exactly are you asking? Should you keep taking it, if it puts your health in jeopardy? No, definitely not.
Speeding muscle recovery and what your body can tolerate aren't related. Whey protein is a great complete protein source, but if your body can't tolerate it, you shouldn't be taking it. That doesn't the fact that whey is a great protein source for repair and growth, or what it can do for you.
Again you could try egg white protein, rather than a plant based protein, or stick with whole foods. Protein powder is certainly convenient but whole foods are also perfect and you'll burn more calories digesting them.
If you have a more specific question, please post exactly what it is you want to know.