For a reasonably common class of deployment and organization (E.g. an online service where the cost of a short outage is significant) it becomes a pain point. For instance if there's a sudden security flap and you need to re-spin your system and redeploy, but that process is gated on GitHub working, now you're screwed if that security flap happens when GitHub is in its 5% down time. Basically you've coupled your uptime to GitHub's uptime in some measure.

I agree with you in spirit, as we have this problem from time to time as well, but number of businesses migrating off-GH shows this isn't the trigger point yet.

More specifically you've coupled the likelihood of your downtime coinciding with githubs downtime. Which as its a product is likely a very small % chance.