Dreamy - yes, if your wife enters as the spouse of a UK citizen after being granted ILE, she can apply for british Citizenship after residing here for three years, and this will not be recinded if she then leaves the UK, no matter how long she is gone for.
If you try to use yout US passport to enter the UK then you won't be able to come in unless you get a visa stamped in it. You could get a right of abode stamp in it I suppose, though I am not sure what the point would be.
Vicky