I wonder if they were trying to avoid the universe correcting itself in the same way Adelaide was always going to die, for example. Maybe they thought if they killed the Doctor it would somehow destroy them since the Doctor was fated to destroy the universe. If they could instead contain him indefinitely they could keep the prophecy forever in a holding pattern.
I think the alliance is going for something
bigger.
The White Dalek says the Doctor will be "prevented" full stop. Not that the Doctor will be "prevented from destroying the universe." He will be "prevented."
The Pandorica is probably a little bit Dalek Void Ship (from "Army of Ghosts"), a little bit time-space crack -- it "unhappens" the Doctor. Thus the Doctor is "prevented," full stop, not just from destroying the universe but from doing anything
ever. It will be as though the Doctor never existed. And even though the powers of the Alliance would be aware of just what effect the Doctor had had upon history, they would also be aware that they would be better off, from their perspective, in a universe without the Doctor's meddling.
Otherwise, why wouldn't they have just killed the Doctor?
"The Big Bang," then, would likely take place in "a cosmos without the Doctor," as the Master so poetically puts it in "The Five Doctors."
And I suspect we'll end up, at the end, in a universe that is
similar to the
Doctor Who universe we've known since 1963, but not
exact, much as J.J. Abrams'
Star Trek takes place in a universe roughly the same, but not exact, as everything that had gone before. The Pandorica is the Doctor's Nero.