It's a player's market this offseason.
While, yes, I'd prefer the Spurs actually retain, let's say, a Ian Mahinmi, and play him, Bonner does offer the ability to provide some spacing for Duncan in the paint with his outside shot (or theoretical threat thereof). I'd rather Mahinmi because I believe that he will prove to be a much better NBA talent than Bonner, and you don't piss away athletic bigman talent.
Assuming the other members of the Spurs' frontcourt are Duncan, Splitter, McDyess, and Blair, retaining Bonner isn't that big of a deal.