It's nothing new in this line of work. I've seen many a dev make major changes for one reason or another. Sure it's not liked by the players, but there is a logical reason behind it, it's just so that they don't have to be made later down the road. It's best to get it out of the way now, rather than putting it off until it's near completion. Typically, those changes are made only once, though, and to be honest, it's not that big of a deal (at least to me, anyway).
As someone who has worked with a dev for as long as I have, and have seen people complain about incompatible saves, it's part of the job. If you like the game, and the dev creating it, it shouldn't be an issue. You'd still support it whether it's an inconvenience or not. Or you could do what most do; wait until the game gets a few updates under its belt before diving back into it. That's why choices are so great. Do I play the game all over again? Wait until there's a few updates? Or just move on to something else and leave this one behind? Either way, if it's the first two choices, you'd still have to start a new game anyway.
