Fortunately, academic users don't need to pay retail. Even students and staff don't generally need to resort to paying retail prices for the Student and Teacher editions, given various agreements available with Microsoft.
Because it just ain't that simple. Some organizations can work brilliantly with FOSS products or operate exclusively in the cloud, independent of Microsoft. However, Microsoft can actually add a whole lot of value in educational markets. Definitely, look at open source options, but know your Microsoft licensing.
The Microsoft party line is that this provides flexibility and, to be honest, they're right. You're best bet, though, is to contact a reseller who can leverage deeper discounts and assist with "software asset management" (how many licenses you have of what product for which users on which machines).