Indeed. With their record at this sort of scale I'd be worried about using Microsoft. And even considering their massive discounts to big business users it would be expensive - though I would write it off as a business expense and get the ordinary tax-payer to subsidise me (and Microsoft).
I'm not sure what you mean by record of scale. Workloads are typically distributed over multiple servers in large enterprises. For example, Exchange is usually spread over dozens or hundreds of servers, and the same is true for domain control and validation. There are some enterprises with well over 100,000 Windows desktops in use.
I hardly think Linux per se qualifies as unconventional nowadays …
On the desktop, Linux is extremely unconventional, with only about 0.1% of the market. That percentage has not significantly changed in years, and unless some fundamental changes occur in the Linux world, the percentage will never change.
On servers, Linux is popular, because (1) it's cheap or free; (2) it has been very heavily hyped, especially by people who have never heard of UNIX; and (3) it looks a bit like UNIX (although UNIX fans will want the real thing, and I don't blame them).
Would it be "better" if I was using FreeBSD (which I considered) or are only commercial offerings acceptable?
Use whatever you want. I run FreeBSD on my server, and Windows XP on my desktop.
No offence chaps but you are all stuck in the stone age. I don't know anybody using anything else apart from regular off the shelf Linux (when not using MS) for anything from small, fairly mission critical projects (radio station) to extremely large-scale web applications that serve tens of thousands of users.
I don't know of any large organization successfully using Linux as a plug-in replacement for Windows desktops. Linux is not suitable for the desktop. The only organizations attempting this are those that are hellbent on "saving money," although there are many pitfalls to trying to move to Linux that can wash away savings and cost a fortune, as many organizations have discovered.
Linux is more popular on servers, for reasons already stated (unfortunately these reasons do not include technical superiority). A system serving ten thousand users is not "large-scale" by my definition, which comes from the world of mainframes. Even my own personal Web site serves thousands of unique visitors a day. A fairly good-sized company might have 40,000-80,000 desktops, a large company may have many more.