The choice of Linux was controversial when Azure was built. It caused a huge issue with the Windows Server team. But it's what customers wanted, and Azure was built very pragmatically.
Yeah they ran on FreeBSD, but despite multiple attempts IIRC they didn't fully pull off the migration until Windows 2000. There was a relatively honest paper they wrote about the transition:
https://web.archive.org/web/20021021164226/http://www.securi...