Okay, so either party (Phil, A&E, GLAAD) has a given right to do what they do. That we know. But the OP addresses an interesting paradox of thought.
Is it intolerant to be intolerant of intolerance? No. Tolerance is a part of what defines our limits, as human beings; boundaries are what we are not willing to exceed or cannot exceed because of our values and standards. It is not intolerant to be intolerant of intolerance.
A man's tolerance can be like steel, it can be heated, beaten, water-cooled and refined. Even so, that still doesn't mean his tolerance is infinite. Steel can be bent, and even broken. Steel cannot exceed itself, not can a man exceed his tolerance before he breaks.
Intolerance of opinion on the other hand, well... a person's intolerance of opinion in this day and age is akin to a piece of tin. It is easily bent and twisted, before too long his intolerance is tolerance, and then back to intolerance. This person's original opinion is lost in the chaos of acceptance. In this case, it is intolerant to be intolerant.