From the cnn article

"Musk became CEO of the combined company and decided it was time for a technological overhaul. Specifically, he wanted to toss out Unix and put everything on a Microsoft platform.

That may sound innocent enough to laypeople but not to Unix zealots like Levchin and his team. A holy war ensued. Musk lost. The board fired him and brought back Thiel while Musk was on a flight to Australia for his first vacation in years."

In Founders At Work, Levchin says

                               " The guy who ran X.com became the CEO, and

I remained the CTO. He was really into Windows, and I was really into Unix.

So there was this bad blood for a while between the engineering teams. He was convinced that Windows was where it's at and that we have to switch to Windows, but the platform that we used was, I thought, built really well and I wanted to keep it. I wanted to stay on Unix.

     By summer 2000, it seemed like the Windows thing was going to happen because Peter was gone. He took a sabbatical to make sure there were no clashes between the CEOs. 

So, this other guy was pushing me toward accepting that Windows was going to be the platform. I said, "Well, if this is really going to happen, I'm not going to be able to provide much value, because I don't really know anything about Windows. I went to a school that was all Unix all the time, and I spent all my life coding for Unix."

I had this intern that I hired before the merger, and we thought, "We built all these cool Unix projects, but it's kind of pointless now because they are going to scrap the platform. We might as well do something else." So he and I decided we were going to find ourselves fun projects. We did one kind of mean project

where we built a load tester package that would beat up on the Windows proto-type (the next version was going to be in Windows). We built a load tester that would test against the Unix platform and the new Windows one and show in beautiful graphs that the Windows version had 1 percent of the scalability of the Unix one. "Do you really want to do that?"

So it looks like what happened was a bit different from what the cnn article implies - that Musk was ousted because he had philosophical differences with Levchin. I doubt the idea of replacing unix with windows on a heavily server centric system was a "philosophical" mistake. Sounds like a typical PHB decision to me.

 levchin actually compared Windows vs Unix performance and even used "beautiful graphs".  :-)