I do hate the "free to play (with gouging IAPs)" model and I actually prefer ads with an option to go ad-free. However even with this business model there are heroes. See for example Path of Exile, a free game in which the in-app purchases do not have an impact on your ability to win: https://www.pathofexile.com/
I do agree with you, the chosen business model makes the difference. I do believe that ads aren't inherently evil, it's just the status quo that is. Yes, today ad-supported means that we are the product, but this product has a free will, a fact that some companies are forgetting. At the very least there are some signs of change. Google for example is at least trying to play it both ways - you can be a paying customer of Google Apps and they'll introduce subscriptions to YouTube for going ads free (with the ability to cache content for offline viewing on mobile devices being the incentive needed for regular folks).
If Github ever pivots to selling t-shirts, run.
Ultimately someone needs to pay some bills though, a few transactions later and this seems remarkably far from their start. It's embarrassing and shocking.
But the underlying point is similar to "you are the product". People chose Sourceforge because it offered free hosting. It was for a long time the "default" choice, back in the early 2000s. They had banner ads, usually from other Linux companies, and that seemed to pay for it. It was easier to use than FTP sites.
The question always remains: who is going to pay for it? If a company is sinking, then they have only two options, to close it down or to engage in ever-shadier chasing of monetisation options. Can you imagine the outrage if they'd put up a paywall? It's basically the same politics as has made "free to play (with gouging IAPs)" the default mode of paying for mobile apps.