Rock, hard place etc.
"A few bean counters can't cope with Linux 'cos they might accidentally see a command line so they need Windows."
Yes, and won't that put said bean counters in a bind?
On the one hand they have been used to the Windows "experience" and had to pay a smallish amount for the privilege. Now however MS has decided "No more mister nice guy" and upped the rates. So where are they going to turn?
Moving to another OS is often a somewhat jarring experience but with the skills of the organisation surely it is not beyond their abilities to smooth the path for those affected.
Remember this is not a SME we are talking about, this is CERN and they have some extremely smart people working there.