Earlier quoted context omitted.
It's easy from an armchair to say things like they should just get more capacity, or they should segregate free repos onto other servers. But maybe they are doing what you're thinking, and with that churn they get mistakes that cause outages, esp dealing with legacy systems. I've been there (not at GitHub or MSFT).
They do not need to make any technical changes. They could make the change overnight: $1 per repo per month (or whatever). This would stop the aggressive growth that they clearly cannot handle anyway. The question is: are they willing to compromise growth for QoS. So far the answer is a resounding: "no". They are deliberately sacrificing the experience of existing users to gain new ones.
I would migrate my 246 repositories before paying even a cent.