I think it’s worth being honest that this upgrade experience was pretty bad but that it clearly was not the result of maliciousness on the developers’ part. I feel this could be avoided by simply showing the changelog screen – and everything that would change, licensing, broken plugins, etc. – BEFORE the upgrade.
1Password does a really good job with this. I understand this is a “for-devs, by-devs” app but a little more UX around the upgrade process would go a long way.
Look to other indie devs like Panic for great experiences here. Lots of warning time, lots of support people available to talk to confused users, and blog posts that highlight the changes coming up.