I agree about Pettitte's limitations as an HOF candidate, but I would point out that I'm skeptical as to the usefulness of Wins Above Replacement (WAR) for purposes of comparing pitchers to hitters. The WAR awarded to pitchers in general is very dependent on how the WAR formula divides up the value of outs between pitchers and fielder -- a division that is more art than science because there is no real objective answer to the question of how much of a relative contribution a pitcher or his fielders makes to outs (strikeouts involve zero contribution by the fielders course, but every other out is harder to judge).
Different WAR formulas do this division differently. For example, the Fangraphs version of WAR rates Pettitte more highly than the baseball-reference version. Fangraphs has Andy with the 10th highest career WAR as a pitcher over the period 1980-2010. B-ref ranks him 19th in WAR as a pitcher over that same period. B-ref, but not Fangraphs, has the following guys with more career WAR as a pitcher than Pettitte: Wells, Saberhagen, Halladay (thorugh 2010), Cone, Steib, Appier, Hershiser. I think Fangraphs rates Andy more highly because Andy allowed an unusually high batting average on balls in play (BABIP) for an elite pitcher (.312 over his career). Fangraphs' WAR formula, unlike Baseball-Reference's, in effect assigns a lot of the blame for that high BABIP to the defense.
The point I'm trying to make (though I've meandered) is that pitching WAR is based on some assumptions that are not relevant to WAR for hitters and thus I personally find comparing WAR for hitters against WAR for pitchers a bit "apples vs. oranges". I find WAR quite helpful (at least as a starting point when combined with other analysis) for comparing starting pitchers to starting pitchers, or shortstops to shortstops, etc. But I'm wary of cross-position comparisons, especially pitcher vs. hitter. Pettitte faced about 13,000 batters over his regular season career, Edgar Martinez had about 8,700 PAs in his career. Edgar was a truly great hitter, Andy was a very good pitcher. Which one was "more productive" or provided his team with "more value" , with their utterly different roles in the game, is a really, really hard question to resolve objectively that just looking at their respective WAR numbers doesn't necessarily resolve.
I intentionally used the Fangraphs version of WAR for the reasons you mentioned--it generally gives pitchers a higher value, which neutralizes the comparison a bit.
It's not a perfect measurement for comparing players with different roles (pitcher vs. hitter for instance), but it is the best measurement I currently know of (even Winshares, when they were accepted, tended to favor batters).
Regardless, I believe that most stats that evaluate a player's overall value will almost certainly favor Kevin Brown over Andy Pettitte and will certainly do the same with future ballot-member Roger Clemens. Unfortunately, as already noted, Brown was already eliminated from further ballots and Clemens will probably have a short tenure on the ballot before the voters banish his opportunity. Pettitte, however, exits the game, we think, as a perpetrator of the same misdeeds and much more rosy reputation.
I think, for the situtation you proposed at the end of your post, the discrepency in comparing the number of plate appearances that batters and pitchers are involved in can be partially resolved with a couple of thoughts:
1. Pitchers will face "easy outs;" whether this be the eighth hitter in the lineup or the opposing pitcher, the pitcher in question will have a certain proportion of his career matchups dedicated to situations that result in an out at a far greater percentage than the average plate appearance. Batters probably have this sort of advantage less frequently (though I have no data to back this claim up), assuming that pitchers who lose these matchups at a far greater percentage than the average pitcher will probably be pulled from the game.
2. Pitchers have eight teammates on the field supporting their cause, retiring the batter, whereas batters do not necessarily have a partner on the field (baserunners could count, I suppose, though I'm not sure if they're as helpful as fielders) and, instead, have nine opponents to overcome in their quest to reach base.