Weren't the Giants tested first (March 3rd)? If injured players weren't tested, then he wouldn't have been. That said, I hadn't heard that exception.
The conspiracy theorist in me wonders how a player can tear something in his knee by banging it on a table. And the $10,000 fine language (and no public disclosure) was in place when the first draft of the agreement was made - meaning it was there on March 3rd. Which could give rise that something may have shown up in his first test, and they fine him and no one knows - and this "Woe is me, the media has made my life miserable" is a cover-up to enable him to serve any suspension under the guise of injury. As far as I know, it hasn't been confirmed he'll miss half the season - just Bonds' speculation.
Anyway, far-fetched, I know. He is 40 after all and athletes don't generally hold up well into their 40s. But he did admit to using the cream and the clear (though he allegedly didn't "know" they were what they were), so a failed test might be possible if they hadn't cleared his system.
I doubt we'll ever know. But the BALCO stuff, the girlfriend stuff, and all the steroids talk makes this injury seem mighty convenient to taking him out of the spotlight.