Certainly consideration has to be given to the supposition that Suppan got himself out of the inning save for Pujol's error. Everything after that is only possible because of that error as the inning should be over. However what if there were only one out, then Suppan become 'more responsible' as he will get charged with more runs of he walks a man and gives up two doubles. What the current rulw reflects is the critical importance of the third out as it introduces a conclusion the inning.

I don't think a pitcher should get a free pass after all the runners have scored who were on base immediately after the error occurred. I say this because, after this point, the primary problems the error caused/prolonged are gone. The way the rule works now, as you point out, the assumption is everything happens should not be the pitcher’s fault because the inning should be over. Now perhaps you can continue to blame the error for additional runners because of the defensive/pitching adjustment made because of the runners on base. On the other end of things, if an error happens with 2 outs, there is a runner on base, the next batter hits a home run so the bases are now clear. There is no excuse after that. At that point, the pitcher would get a free pass on earned runs for no other reason than because the batting order had changed. If that is the case, he should get a free pass on earned runs the rest of the game.
Just my thoughts as a less informed baseball fan. I am interested to see what your regular contributors have to say

I think a bigger problem is the official scoring of a game. For example, Clemens is charged with a run because his shortshop drops the ball behind 2nd base and Womack is credited with a hit. Granted, he's a fast man, and the announcers said nothing, but at the time, I was thinking error the whole way, and the look at Vizcaino's face matched it. The replays didn't change my mind, but then, they don't show you a simultaneous view of the runner going down the line and the fielder. Then, in the inning in question, Pujols is charged with an error on a tapper to first. From the replays, I don't think he or Suppan could have beaten Beltran to first, Suppan and Beltran were basically neck & neck at the point Pujols mishandled it, and Beltran is faster. Definite signs of "hometown" scoring to me. I've thought for a long time that baseball needs to revisit how the official scoring is done. Back to your point though, I agree with the thought that only if the error directly leads to a run (either the run scores on the error or the player who reaches on the error comes around to score) should be unearned. However, what would happen on a situation where a runner on 1st, no outs, goes to third on a fielding error in the infield, then the next guy picks him up with a ground out or sac fly? The error indirectly lead to the run, he wouldn't have scored from second.

Just eliminate the error as a stat, it's a silly idea anyway and count all runs as earned all the time.