Stack Overflow wasn't developed by an established software company. It was a completely new startup, founded by two high-profile (at the time) software commentators.
They could have hired people to use any stack they wanted. While the state of web development wasn't what it is today, OSS stacks such as the LAMP stack were fairly well-understood and popular.
It makes total sense why the tech is what it is. One could argue they could have shifted away from that stack since then, but one could also easily argue (very convincingly to anyone who has ever been involved with any significant project rewrite) "but... why?".
I'm not arguing that the licens isn't a concern, I just question how much of a concern it really is, compared to everything else.
Of course, the OSS stack costs nothing to acquire, is cheaper to admin, and will give you more functionality and easiness of use, but the MS one isn't some unaffordable monster like other proprietary ones.