Not to toot my own horn, but so far I've been on the same wavelength as Moffat.
There was only one reason for a married couple in the TARDIS. In the UK, this is a children's show. In a children's show, in order to remove any possibility of scandal, it's necessary to marry the characters. Rory and Amy were married to produce River.
Similiarly, there is only one reason to marry the Doctor.
I think Clara's identity follows logically if you wonder why, after almost fifty years, they would marry the Doctor.