. . . which explains why Gore is now in control of the DNC . . .
He was in control of the DNC. Joe Andrew, McAuliffe's predecessor, was Gore's guy. Had Gore won, Andrew would probably still be there today. McAuliffe was supposedly slated to become Ambassador to the UK in a Gore Administration.
When Gore lost, everybody started looking ahead to 2004, and they didn't want Gore's guy there. Clinton's guy looked safer, because Clinton can't run again, and nobody figured Hillary for 2004. It is true that Clinton pushed on Gore's guy, but it was Daschle and Gephardt who shoved him out.
You're right that the same thing could happen again, but probably not. Whoever the nominee is will presumably replace McAuliffe with his own guy. If he loses, his guy could indeed get rolled, but The Return Of McAuliffe is an unlikely outcome. For the 2008 cycle, everybody will know that Hillary is coming, so her guy isn't gonna get it.
To some extent, the Clintons have power because people think they do. That's why the current moment is Hillary's best bet. A lot can happen between now and 2008, including the emergence of some new "power" in the Democratic party. If the nominee is someone with a little more star power than Gore, he might not be so easy to knock over, even if he loses.
There is also the issue that the Clintons are perceived to be part of the DLC wing of the Democratic party. To the extent that the liberals take over the joint, Hillary will lose influence, and may even come to be seen as an emblem of the failed past. I suspect that she is personally a lot more ideologically liberal than Bill ever was, but she might not be able to shed the DLC baggage. It may be that she has to move now, or forever lose her chance.