Well, I'd rather their attempt at writing to my shell config breaks.
This is one of the many reasons why you should, if you haven't yet, manage your dotfiles with version control. Many tools assist in giving you some sugar over the process, I use homeshick which will move files away into a git controlled folder and create symlinks.
$HOME/.ncmpcpp -> $XDG_CONFIG_HOME/ncmpcpp
The correct way to handle this, for any projects forcing the change, is to use a staged deprecation period:
* first, you add support for XDG
* second, wait at least one version to give people time to get used to it
* third, switch the config location search order so it checks XDG before .whatever
* lastly, after an announcement and deprecation period, and at least 2-3 releases, remove support for the .whatever folder.
(To be fair, it's totally possible that my upgrade path with ncmpcpp skipped over some steps and they actually did it correctly. Will have to check when I care enough to dig through commits.)
That way you can introduce the new guidelines while not breaking stuff to those who want the old bash.