I'm really surprised by this as well. These mistakes were exactly the same ones that ZenDesk made. Obviously they didn't take the time to learn from that particular fiasco. Had they paid attention to ZenDesk's problems, they would have avoided almost all the problems they had.
As a counter example, I signed up for Backupify during their beta. I recently checked their site and saw that their free plan is fairly limited, but my account shows I'm at the premium level, which currently has a monthly fee, though I pay nothing. They grandfathered in my account without even telling me there was a pricing change. In other words, only new customers were affected, not existing customers. There was no uproar because it didn't really affect existing customers.
I think the thing here, would be to grandfather paying customers, as they are already paying you and you can determine their expected value to make an educated choice about them.
Grandfathering existing customers seems like the only logical path if you really want to hike costs of a subscription.