Also it's worth noting that github's entire UI, at least for browsing (I didn't try creating an issue or editing a file), works just fine with javascript disabled.
Even if you can connect to GitHub without ever touching their proprietary JS, that's clearly not the typical route. Just like you can connect to Slack using nothing but open source clients, but one is "enticed" to use the proprietary client.
You can clone/pull anonymously from github and eg: email patches.
I'd say using github just for hosting read-only/read-mostly git is a bit like running http on IIS or email on Exchange - or indeed a propietary XMPP server that allows federation.
I'd prefer Free projects to use Free infrastructure - but building on established open protocols is good. Contrast with bitkeeper: you'd have to reverse engineer the protocol to pull/push - or with slack: there's no way to set up your own server snd federate with it.
So OK, sure, github is as bad as slack.
Actually it's not completely irrelevant, as the fact that the host platform of proprietary software is free software has value in the security-based argument in favor of free software, but that's only tangential to the topic at hand.
Would it also be bad to host the project's source code on GitHub
Not necessarily, if really all you're using github for is hosting, then there's nothing wrong. That is, if you don't use their issues/PR system or other auxiliary services. This is how, for example, the linux project uses github. In this case, all that you're asking people to do is use git (free software) to download some stuff from servers owned by Github, Inc.
Running the website on IIS is fine though; this imposes absolutely nothing on your users or contributors.