If you look at the period when Lee played his stats are a little less impressive. Same with Gibson... they both pitched during a very dominant pitching era. Not trying to take anything away from either of them of course.
As for Lee... he's still really damn good. The Giants were just zoned in/lucky that night. The balls Cliff was "leaving up" look bad compared to his previous start, but that's because his previous start he basically had Rivera-like control. Most of them were pretty near the corners, and at least one of the doubles was on a perfectly placed pitch. It's just the usual second-guessing and "hindsight is twenty-twenty" thing. I know for a fact that a ton of our pitchers leave balls up and none of them have a BABIP above .500. Of course, we don't have Guerrero playing in RF either.