I think Phil has every right to say what he believes, and at the same time A&E also has the right to do what they did too. I don't know what A&E's contract actually says, but often there is something like a code of ethics that the people must follow, even while not at work, esp. when it is in the public eye and can affect the network. I think part of the problem is that the average viewer of A&E in general is a little more liberal in terms of sexual orientation, so the network felt that it needed to do something in order to keep those viewers, even if that meant perhaps sacrificing the show's ratings.
I'm more amazed by how shocked everyone seems to be over this... Anyone that has watched the show knows that the Robertson family is very religious (I think they end every show with the family gathered around a dinner table and praying together), and as most Christian denominations condemn the act of homosexuality there was a great possibility that their beliefs would run along those lines. And since this is a reality show, the network also ran the risk that the beliefs held by the family may conflict with the views of the network.
I haven't actually read the entire article, but I did read some snippets that were included in a Huffington Post article on this issue, and one of the things that I noted was that Phil was asked what he considers a sin, and he went on to talk about sexual immorality in general, mentioning homosexuality, but also mentioning bestiality as well as what I perceive to be promiscuity (the quote doesn't mention this exact word, but he said "...sleeping around with this woman and that woman and that woman and those men." which to me describes promiscuous behavior). People were quick to point out that he compared homosexuality to bestiality, but then failed to point out that he also compared it to promiscuity as well. He was just giving a litany of what he considers to be sins, not that he believes that homosexuals also participate in bestiality (which I think is what some people were trying to insinuate). Moreover, Phil also mentions how we're all sinners, and that it is not our responsibility for deciding who goes to heaven but rather that is God's judgement. He goes on to say that he wouldn't judge or treat a homosexual person any different just because of their lifestyle. This I think dovetails with a Christian axiom: Love the sinner, hate the sin.