First of all this should have been taken care of in 2000 during the World Series. It was not, and I find that to be the problem. Sure, this is the first time that he has batted since that bat incident. But issues have to be settled on the field as soon as possible, and the Mets did not do that.
I learned early on that on the field issues (those unwritten rules) need to be settled as soon as possible.
Second the Mets are about six to seven games behind the Braves in a division that many expected them to win. So they needed a win badly. With Clemens being by far the weakest hitter as far as I am concerned in a very strong Yankee lineup, I would not have hit him. Why? I would not have because then the lead-off batter comes up and could possibily advance Clemens and/or drive him home. So in essence the strike out was better.
Consider that the Yankees lost 8-0, and Clemens went out in the six with a bad foot. It was not a good day for Roger.
HOWEVER, I would have thrown a pitch to cause him to duck or be brushed off of the plate. Trust me. Those kinds of pitches send strong messages. Yet, the brush back pitch and pitching inside are missing from baseball. One can intimidate a hitter without hitting him. Some pitchers have forgotten that.
Note that only seven present Mets, including Estes, played on the their last World Series team.