The ICT_Works blog has come out swinging: Linux vs. Microsoft is the most useless debate in ICT4D
As would any sane-minded person after being subjected to a shouting match in Kyrgyzstan. And the core point is absolutely valid - when you're talking about educational outcomes, there is no effective difference:
Educators stressed that teachers already had extensive training on Windows software and would be confused, even lost, in the Linux environment. Students who learned Linux and LibreOffice would be at a disadvantage in the job marketplace as employers would only hire staff that are fluent in Microsoft applications. [...] All of the adults in the conference learned how to use computers back when Windows 98 was in vogue, some even started with Basic, yet no one complains they cannot use an iPhone, iPad, or even MacBook without training.
Where bandwidth permits, much of a computer's purpose is to provide a browsing window onto the Internet. So unless you've selected some Silverlight web app as your central educational portal/experience (Or, if you want to use iPads, anything in Flash); you're really OK. The minor differences for the user between the different OSes becomes a habit you learn (though admittedly, to this day, Mac's multi-file-select using keyboard only, kills me). Now, I would argue that for a real programming learning environment, MS vs Linux really does matter - coding ASP.NET on Linux is a royal pain, and coding, well, anything else on MS is unpleasant to actively nauseating. But for most education outcomes, the technology doesn't - and shouldn't - matter. But for a lean budget and long-term or self-sustaining program, the differences bear more scrutiny.
Sustainability has a strong voice as to what platform you choose for a project.
There's an obvious support/infrastructure case - if your entire administrative capacity (be it that one volunteer who comes in every other Thursday or the entire tech support department of a Ministry) uses and is comfortable with only one technology, then you better have a very strong reason to not use that. It's path dependency at it's worst. Deal.
If your budget is robust enough, you have a long-term committed donor, and are getting systems that already include the cost of both Windows and an Office suite, then peace be with you. For a decently funded project that will be re-buying their computers every 5 years, give or take, this may not be a challenge - the new computer will come pre-installed, for a minor extra fee, with all the MS and Office programs you'll need, and they may even be legal versions. Governments do get uncomfortable visits from their friendly local software licensing lawyers, and there is costly lock-in danger for a lot of non-free software.
For a project that's buying custom-built computers from the guy around the corner and hoping to get 8-10 years of use out of them, doubling or tripling the cost of that computer to add a legal copy of Windows+Office ... and opening up a costly path into anti-virus, anti-malware, and ongoing maintenance to remove the various random toolbars, searchbuddies, and porn popups that magically appear over time (protip: remove all traces of IE that you can. Install Chrome. Label the Chrome shortcut with a blue "e". )
Going much deeper here opens up technical platform differences that apply mostly to edge cases, and are the exact kind of arguments that fuel yelling matches, so I'll end with a reminder - look at the realistic project lifespan and budget, look at the ongoing maintenance costs for any platform, and your support networks available. Don't get caught up in OpenOffice vs LibreOffice vs MS Office vs Google Docs/Drive, or whatever the daily this -vs- that debate is. Focus on outcomes and sustainability over the project's lifespan.