Unless this is a Mono port of stackoverflow and it is running on Ubuntu server.
(Ubuntu's bug #1 is that Microsoft is more popular than Ubuntu - see at https://launchpad.net/ubuntu/+bug/1 )
If you read Bug #1 closely it's that
Microsoft has a majority market share in the new desktop PC marketplace. This is a bug, which Ubuntu is designed to fix.
This has nothing to do with Servers, as I (unofficially), estimate that Linux Servers far out-weigh those of Microsoft and Apple servers. So having the StackExchange platform run on a Microsoft stack isn't so much detracting from Bug #1 - but rather is helping resolve Bug #1 by being able to provide this magnificent platform for which to offer support for Ubuntu related questions.
Even Canonical makes software for Windows. See the upcoming Ubuntu One client for Windows.
askubuntu.com isn't here to fix bug #1. We're here because we like Ubuntu and want to help others learn Ubuntu.
Be careful with religious attitudes, Ubuntu is just one tool among many. Use what you think is the best tool for the Job. If the SE developers want to use a Windows platform good their application, it's because they think it's the best tool for them. And we benefit, because the SE sites are a great application. I say this as a Unix user for 19 years, and a Unix admin for 10 years.
If you feel that you can do better with an Ubuntu-based platform, then good!
Leaving my opinions aside:
It's the best tool for the job as it is the most mature and polished. A good user experience is part of Ubuntu's purpose so it makes sense to make decisions to support that.
Ideally, using proprietary software is only acceptable when one is writing a free replacement for it. This site is not being used to write its free replacement, it is being used as a supporting tool for users of another free program. Is the user data under Canonical's complete control? No. Is it under the users' complete control? No.
However it is CC-BY-SA licensed.
It's the same old "Open Source" vs. "Free Software", Pragmatism vs. Idealism, Best-Tool-For-The-Job vs Free-Tools-For-The-Job arguments this community will always have until all software fits both categories.
I'm here because the users are here, and yet I'm also on other sites because I want the users there.
Ubutnu Forums are the official forums for Ubuntu-related help, support and discussion. It runs on proprietary software. The main aim of this site is not to promote particular types of software but being a useful resource for the community. And I think that the StackExchange model is very useful for getting your questions answered.
I don't know anything about the infrastructure of either askubuntu or Stack Exchange (other than the software is open source), but don't think picking a tool simply out of principle is practical for a large project such as this. When it's just you and your desktop running tools for yourself, then you should feel free to use whatever floats your boat, however when the project is a site like this, then you have to consider the users before yourself, and whether or not using entirely open source tools will have a positive or negative impact on the user experience, and thus on the quality of the support they receive. If Microsoft provides the best possible tools to that end, then that's something we're just going to have to live with for the time being.