A professor at a Christian college claimed to be in religious solidarity with Muslims. That’s pretty much like saying that you’re attempting to further Facebook’s goals as a Google employee. Of course you get fired.
Different religions are going to have angry doctrinal differences by definition, but you can't let that obscure the obvious. We're not talking about tengrism or Brahma here.
I'm not sure if the greater theological offense was the solidarity with Muslims or quoting the Pope in support of it (Wheaton had only a few years before fired a professor for converting to Catholicism; “Christian” isn't a label of a monolithic group in practice.)
This comment is a fine answer to your ideas: https://news.ycombinator.com/item?id=26311621