However, it sounds like the organization in question was not deploying to Windows - from the article:
...it seemed to me that most of your development happens on Windows (though it’s almost needless to say that you deploy to Linux)
I won't judge you for using Windows over Unix (even though I prefer Unix), but I will judge the choice of using Windows for development when you are targeting Unix. I have had this experience, and it was a Management decision - not an Engineering decision, and it resulted in significantly less productive work environment. Given two opportunities that are otherwise equal, I would definitely choose the company that develops on the same platform that they deploy on (assuming we're talking about Unix or Windows - there are obvious exceptions in the embedded world).
One caveat: It is common for an organization to use both Windows and Linux for different tasks. In that case, the choice of development environment is more complicated.
Either way, I'd say that the candidate should have asked up front during the interview, "Why are you using Windows for development, and could I use Mac/Linux instead?", instead of judging them based on what seems like a lack of information. They may have a good reason. If they don't, your decision is that much easier.