It's hard to see the difference between selfish behavior and short-sighted behavior because they're often confounded. What I got from this is that Alloy will consider the deep vs shallow deep copying Git issue, but wants to continue using Git and GitHub as a CDN for a massive user base, and doesn't want to re-architect because developers are expensive and time is limited.
The Git deep v. shallow issue just puts a band-aid on the CPU problem, but it doesn't do anything about the terabytes of bandwidth per week (it'll be worse), and it won't do anything about GitHub's claim that Git is not meant to be used as a CDN and doesn't scale well.
They've become a big project that warrants thinking about revenue or organization strategy, but they're delaying it by externalizing their costs. Cases like these can pressure GitHub into rethinking the leniency of their policies.
I also think that if you're in the top-5 resource consuming group, more sympathy would go your direction if you were a paying customer, but they've indicated no interest.