I just got my usb Bluetooth dongle about 2 hours ago. It’s an ASUS USB-BT400. I disabled the internal bluetooth as per your instructions and restarted and then my controllers paired immediately with the new bluetooth adapter.
You can check to see which adapters are active using hciconfig.
I’ve been playing for about 2 hours and am glad to report that I had no freeze until now. It’s great to know that the problem was caused by the PI’s internal bluetooth, because at least with a USB dongle you can get around the problem, and I’m sure that the rPI foundation will eventually find a solution.