They're going to stay together but it won't be a smooth road(as expected).
Fox will blame the ratings drop on House and Cuddy getting together but that isn't the whole problem. The problem is their new relationship is getting way too much attention. It's been the main plot point of every episode this season. They need to drop stuff in there for the 'Huddy' fans while not making people who couldn't care less turn the channel. It's tricky and they need to be more careful with the writing.
Minor spoiler but better safe than sorry...
Spoiler: show
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