The criticism against CocoaPods here seems awfully harsh.
Think about it from their perspective. GitHub advertises a free service, and encourages using it. Partly it's free because it's a loss leader for their paid offerings, and partly it's free because free usage is effectively advertising GitHub. CocoaPods builds builds their project on this free service, and everything is fine for years.
Then one day things start failing mysteriously. It looks like GitHub is down, except GitHub isn't reporting any problems, and other repositories aren't affected.
After lots of headscratching, GitHub gets in touch and says: you're using a ton of resources, we're rate limiting you, you're using git wrong, and you shouldn't even be using git.
That's going to be a bit of a shock! Everything seemed fine, then suddenly it turns out you've been a major problem for a while, but nobody bothered to tell you. And now you're in hair-on-fire mode because it's reached the point where the rate-limiting is making things fail, and nobody told you about any of these problems before they reached a crisis point.
It strikes me as extremely unreasonable to expect a group to avoid abusing a free service when nobody tells them that it's abuse, and as far as they know they're using it in a way that's accepted and encouraged. If somebody is doing something you don't like and you want them to stop, you have to tell them, or nothing will happen!
I'm not blaming GitHub here either. I'm sure they didn't make this a surprise on purpose, and they have a ton of other stuff going on. This looks like one of those things where nobody's really to blame, it's just an unfortunate thing that happened.
(And just to be clear, I don't have much of a dog in this fight on either side. My only real exposure to CocoaPods is having people occasionally bug me to tag my open source repositories to make them easier to incorporate into CocoaPods. I use GitHub for various things like I imagine most of us do, but am not particularly attached to them.)