I haven't read book 3 or any of the Warrior Cats books in quite some time so I'm not sure whether or not Firestar had permission to take Cloudpaw to his mother but I'm sure he didn't.
I don't think Erin Hunter is trying to sell us on the fact that kittypets are better than clan born cats but more to the fact that kittypets can be clan cats, period. If you notice, in the first book, Firestar catches a lot of **** for being a kittypet and continues to do so throughout the series. Even after he becomes leader there's a bit of a problem with some clan born cats who don't feel he'd be a good leader just because he wasn't clan born.
It's not about which type of cat is better, it's about the fact that kittypets aren't as weak as clan cats believe them to be and that they can pull their weight too.
The decision to bring Cloudpaw into the clan was well founded, I believe. Princess didn't want her son to be a housepet and she saw her brother doing well and living happily with his clan and that's what she wanted for Cloudpaw. While it may not have been cleared with the clan first, Cloudpaw has proven to be a very nice addition to ThunderClan and he's very loyal, albeit a little reckless. Besides, after Firestar there will be another clan born leader - last I read he appointed Brambleclaw - Tigerstar's son - as his deputy, so fret not.
Unless there's been a big change in the clan line-up between the ending of "The New Prophecy" series and the six books that follow, clan cats still outnumber kittypets, I don't know where you heard that there are too many.