For most organizations, especially non-technical organizations, the availability of source code is really irrelevant. One might argue that they *could* change things if they needed to, but as a practical matter they really can't. Organizations whose mission includes software development are certainly capable of taking advantage of free and open licenses.
But it sounds like the bottom line is that, in the end, they found Windows better for them than Linux. You certainly have to admire their willingness to try something outside the norm, however. IT wouldn't have made much difference, I suspect, if Windows were open source and Linux were proprietary.
Unless you're a software development organization, source availability per se is really not a useful criterion upon which to make an IT decision.
But this is Slashdot, so, you know, it must be a conspiracy.