I don't think that Anora is necessarily looking at the situation like an amoral politician would and craving her own personal power above all else (although she might have considered it), but rather what she thinks is best for the country and those who would be her subjects.
Like her father, she's got a stubborn and prideful streak that can sometimes get the better of her, particularly when she forms an opinion of something or someone. Both Anora and Loghain are people who hate to be wrong, find it difficult to consider that they might be, and have an even worse time openly admitting it to others.
From her POV, putting Alistair on the throne alone is putting all of Ferelden at risk. And frankly, I think she's right. Even my Wardens who took issue with her attitude accepted the fact that with her on their side, the Landsmeet is a slam dunk, and a united Landsmeet means a stronger Ferelden. A political marriage between the two of them is still the most practical option, and one nearly every Warden I have takes.
In my opinion, anyone who puts Alistair on the throne by himself is not thinking straight. Anora can only make the throne stronger. There's no logical reason to take her off the throne. Again, in my opinion.
This is part of the reason I often debate whether or not to have Alistair rule jointly or seperately.
On the one hand, Anora can bring a lot to strengthen Alistair's rule and it would make a far more stable country without any dissent from those still loyal to Anora. On the other hand, she brings her force of personality with her and that might be detrimental as well. If we're to believe her account of her marriage to Cailain, she's already gotten used to ruling the country while Cailan enjoyed skiving off to do whatever peaked his interest... or whoever peaked his interest, if he was unfaithful as she further claimed.
It's therefore possible that Anora's backseat driving might cause Alistair to become lazy and slack off, which we do see happen if he's unhardened, according to that particular epilogue. On the contrary, Alistair ruling by himself gives the potential to have even more of a push to greatness, free to forge his own path without outside interference from those with their own ways of doing things. Keep in mind, Anora does comment on a hardened Alistair being eager and willing to learn.
It's not to say that Anora is a bad ruler, but she's grown up in that world and would likely want to see the status quo maintained, since it's the way it's always been done and it's worked well enough so far. Alistair meanwhile seems to favour change and has seen Ferelden from the perspective of the common people, struggling to get by. He knows that the system in place is not perfect and we constantly see him ask the Warden to help people throughout the game, so as a ruler, he'd be more sympathetic to the poorest of his subject's plights.
Of course, this is the difficulty of the decision, because both have their merits and both have their flaws?