Hard to say without knowing what your specific knee issues are, but I'm in the process of rehabilitating one of mine. I do the lunges and squats slowly with hand support. I also don't go as far down.
Chocolate does have added sugar, but it's also good for you. The DBurn article on sugar suggests that if a serving has less than 10g of sugar, then it's ok. I buy the dark chocolate with a high cocoa content, NO artificial ingredients and a low sugar content and eat it sparingly, as a snack, with raw pecans or walnuts.
I'm using egg-white protein sweetened with stevia. Eggs are not excluded or recommended in the Ignite program, and one of the other threads suggested it was an acceptable alternative as long as it doesn't contain any sugar or artificial ingredients.