Well, I'm a big Debian user too. I don't care what the actual configuration format is, but I do like stuff in /etc/default.
That said, I don't think putting locale.conf in /etc is that big a deal. There's plenty of other system-wide conf files in there; there's never been a full transition. The timezone file is in /etc, as an example, and I'd call that almost exactly identical in scope. I see no logical reason for timezone to be in /etc, with locale in /etc/default, but that's how it presently is. It seems likely to be backward compatibility driving that choice, rather than technical merit or logical consistency.
Like all other flavors of Unix, Debian is sloppy about where it puts configuration.... look at all the crap under /var/run, as an example. As much as I like it, and as much as I use it, I don't think we should try to paint it as the shining city on the hill. It's actually quite messy.
In this particular case, I guess I'd just sort of shrug and use symlinks. We can either stick them in default and link to them from /etc, or the other way around. I don't see it as being that big a deal.
Yeah, maybe it's a little rude on Poettering's part, but meh, not worth worrying about that much. Adding one more tiny inconsistency to a distro that already has so many doesn't strike me as a major aesthetic affront. You can argue that we'll never get to the hill if we keep moving away from it, but I don't think a symlink is really moving away.
That said, it seems a little silly for Poettering to refuse a patch to look in one more directory.