Hi, did you manage to resolve this? I have the same problem and same situation (pihole running, can ping github from ssh container).
Edit:
I was finally able to resolve the issue.
First step, it was a simple mistake, as stated in PiHole addon doc “Ensure your Hassio device has a static IP and static external DNS servers!” https://github.com/home-assistant/operating-system/blob/dev/Documentation/configuration.md
I thought I already did that but I recently redone my HA install and forgout about it since I also had a DHCP reservation with the same IP
Then following this comment Updater Problem: Exit Code 128 - Could not resolve host github.com I fixed the problem setting the PiHole > Settings > DNS > Interface listening behavior option to Listen on all interfaces instead.