I think both companies are to blame, but keep in mind that they both were trying to make things better.
GMail is non-standard, and no regular IMAP mail client works 100% correctly with it. (See other posts in this discussion where people try other solutions. Nothing works perfectly, not even the non-free mail clients.) But GMail's changes are pretty good ideas. (Why should folders be exclusive? That's leftover from using a filesystem as a database. And there's no need to duplicate emails on disk, just have the folders contain message IDs.)
Apple Mail worked pretty well pre-Mavericks, but only if you had the settings just right. With the release of Mavericks, Apple tried to improve GMail compatibility, but apparently they didn't test well enough.
My guess is that Apple will have to do a lot of work to fully support GMail, and this might mean significant changes to the Mail program. What they tried to do was a simple fix, and GMail is just too different for that. (I suspect there is a developer or two at Apple who is now saying "I told you so" over this.) For example, that label on the right of the message which says which folder a message is in (e.g., when viewing by thread) will now have to list all the folders that the message is in. This is GUI change!
Anyway, the rumor sites say that Apple is beta-testing a fix to this problem and plans on distributing it soon. We'll keep our fingers crossed.
Bark!