I think they paid him that for reasons that Solid D stated, but also because this should allow Duncan and McDyess to play slightly less minutes, but more importantly sit out more games entirely next season.
The fact of the matter is, if Duncan goes from 31 to 30 mpg and McDyess from 21 to 18 mpg, sure it should help some, but it's not going to make a drastic difference in the grand scheme of things.
What Duncan in particular needs is to have the minutes he does play be less arduous. That means not playing small ball with anywhere near the frequency the Spurs did the first (roughly) two thirds of last season. But it also means sitting out more games.
Looking past next season though, is another major reason I believe the Spurs re-signed Bonner. If they let him go now, then a year from now they'd be searching for his replacement to replace McDyess in the rotation. I can't think of another readily available 40% three-point shooting big who makes in the $3-3.5 million range.