How about $999.99 (same as Adobe Photoshop so it should only require middle management approval)? What if you got a box like the yellow google search box (it could be called that the "premium version")?

An unknown factor in all this is how many companies would be even interested in buying a github server in the first place. If it isn't that many the costs might be too low to sustain development. I am betting that for the GitHub guys it makes a ton of sense for them to sell the private small accounts on github (and only manage/fix 1 github version). and for the big guys sell them a big package.