Well, the guy is 36 years old. Unfortunately, for all-natural players, that tends to signal the end- particularly if they've got a hamstring held together by bailing wire and staples. But you're right. The Manager positions the players in the field and controls where they hit in the order. Griffey is the Reds' Center Fielder because he has been chosen to be the Reds Center Fielder. He hits in the three-slot because that is where he's written into the lineup.
The OF should be Griffey in LF, Dunn in RF (before he eventually moves to 1B), and Freel in CF. It sucks to see a hero's defensive skills disintegrate, but that's what happens. Even Andruw Jones has lost steps, but the Braves still run him out to CF based on his reputation.
At the Reds have broached the changing positions topic with Griffey in prior years. At this point he certainly shouldn't be adverse to switching excepting the idea the fast stops at LF (the only other OF position he should play) and stretches at 1B would strain on his already-debilitated hammys. If he's incapable of playing another position, then he's a DH playing Center Field in a league that doesn't offer the DH position.
And hopefuly you now how hard it is for me to say that about Griffey. I've been full-on in his corner while he's overcome serious injury problems. But at some point he and Reds management needs to realize that a position switch is in everyone's best interest.