> So not balking means being willing, right?

In this case, willing to proceed with what he was planning to do, that is, moving from Windows to Linux against Microsoft's wishes.

edit: And you're right that this implies "balking at Microsoft's proposal". Personally, I did read the sentence as intended ("they wanted him to balk (= stop his plans), but he did not"), but I can see how the phrasing can be misleading...