As Miranda is the main star of iCarly, she's entitled to have a say on those things.
And just because she thought of (15 years old) Nathan Kress as not sufficiently hot or attractive for girls, it doesn'tmean she ever disliked Nathan as a person. Now that Nathan has grown more into a manly man, Miranda may have changed her judgement, and she thinks of Carly/Freddie as a great thing. It's still all to be left up to Miranda, as she already sang three years ago.