I understand Heroku's decision, but I must say, when the opposite happened to me with SendGrid a couple of days ago (I didn't even asked for the refund, they did it on their own initiative), I was extremely positively surprised.
Right... But I've heard nothing about your experience. Likewise, there is a nonzero likelihood that Heroku could give this HNer a $1000 break and get no publicity...
For $1,000 and no publicity that would still be a valuable lesson learned.
What's more interesting is if this happened before and how they dealt with that. What's the cut-off point at which you want to stop your customers from doing serious monetary damage? $1000? Apparently not. $10,000 ? $100,000?
There comes a point where the continued existence of Heroku would be at stake, so it is in their own interest to guard against this, especially when you take in to account the number of users they've got.
They need some guardrails for this, and sooner probably better than later. Terms of service will not protect you if your customer can't pay your insanely large bill.
In that case you'll end up eating the charges anyway, so guardrails are to mutual benefit.
In my opinion, your point is totally orthogonal to the point I was responding to. I agree with your reasoning about Heroku's self-preservation completely.