Suppose for a moment that Jr. bucks the odds. He has a healthy 2007 AND 2008. He puts on a power display, 40-45 HR's both years. That would give him close to 650 career HR's Would you pick up his 2009 option?
Remember, baseball isn't a vacuum. IF Jr. were to accomplish this, it puts him in spitting distance of 700 HR's There is some good long term PR to be gained from letting him finish his career in red. Similar but different to letting Larkin retire a Red. The media begins to follow him around, and even though Jr.'s rep with the press is rocky, it ain't Bonds' rocky.
Now of course I fully expect a half a dozen posts telling me Jr. won't be healthy for the next two years. Please remember I did say "Suppose."