This is not just about homophobia but about being objective which is what gives newspapers their credence.
The article states that: "He ranted further:
[Jesus] said there would be deceivers. He said those deceivers would cause Christians who remain true to His teachings to become reviled. He said false prophets would follow to deceive even more, and that lawlessness will abound."
That phrase particularly, "there would be deceivers", works against being objective because it shuts down conversation. It says, here's my point of view and any other point of view is invalidated because it counters my point of view.
That might work for a blogger, it is pretty much necessary to a religion, but not appropriate at a newspaper of any creds, certainly not when exhibited publicly.
The firing is entirely just.