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.
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.
Some Free Software people certainly think that. It is imho at least problematic. For example, the unicorn web server developer, finds github problematic from the 'UX' side in addition to dependence on proprietary software and infrastructure (which creeps into the commit messages).
"Contributing to unicorn is socially as easy as contributing to git or the Linux kernel. There is no need to signup for anything, no need to ever touch a bloated web browser."[0]
[0]:http://bogomips.org/unicorn-public/20140801213202.GA2729%40d...
The web browser may be free, but all of the JavaScript you are running is proprietary.
>And there are many closed-source IRC clients.
But there are many free ones, and there isn't an official client that is proprietary. It's possible to use Slack, more or less, over IRC or XMPP, but they are second-class citizens. The recommended way to use Slack is via their proprietary web interface.
And even if the JavaScript files were not minified, they likely aren't available for user modification and redistribution because they are protected by copyright and a license that says "all rights reserved."
I'm no fan of Slack, but I don't get the claimed conflict when using it with an open source project. Would it also be bad to host the project's source code on GitHub, or the web site on IIS?