I would tend to think that there's something special about the Portrait Gallery in the Headmaster's office. After all, the portrait of Dumbledore that appeared upon his death was hardly the first picture of him. I suspect Harry will be doing a lot of talking to Dumbledore's portrait, and wouldn't be surprised if the portrait tells Ms. McGonagall when it's time for Harry to learn the truth about Snape.
They may very well make McGonagall the new Headmistress of Hogwarts, but I am beginning to doubt it.
Scrimgeour is apparently not a big fan of Dumbledore's, and with MM being a good friend and collegue of DD's, I am not so sure they will allow her to take over permanently.
Besides, it would be a nice little plot device to make it a bit more difficult for Harry to be able to talk to DD's portrait. He's growing up, and DD was preparing Harry to act on his own as it was, before he was killed.
Prolly just a silly idea, but hey...JK is fond of throwing obstacles in Harry's path for him to overcome.