As an empirical question, I think you are likely right that charging off some money owed might buy Heroku disproportionate amounts of goodwill. (I do it all the time.) That is, properly, their call.
As a normative question, though, for-profit businesses do not have a generalized right to make their mistakes into others' obligations.
More broadly, one of my periodic crusades is trying to get HN people to understand that norms in the business world are very unlike the norms of cash-strapped twenty-somethings regarding things like a) the appropriateness of charging money (charge more) b) how much money $1,000 really is (a lot to you, a lot to me, rat spit to businesses with an HR department) and c) expectations for professional behavior (you're doing taxes like a boss, reading contracts like a boss, capacity planning like a boss, paying your invoices like a boss, etc).
As a normative question, though, for-profit businesses do not have a generalized right to make their mistakes into others' obligations.
More broadly, one of my periodic crusades is trying to get HN people to understand that norms in the business world are very unlike the norms of cash-strapped twenty-somethings regarding things like a) the appropriateness of charging money (charge more) b) how much money $1,000 really is (a lot to you, a lot to me, rat spit to businesses with an HR department) and c) expectations for professional behavior (you're doing taxes like a boss, reading contracts like a boss, capacity planning like a boss, paying your invoices like a boss, etc).