Rather than eliminating data points, just cap the number of runs that you use at some number (11, 13, 15, whatever). Above a certain level, it really doesn't matter.
You could probably adapt something like what the USGA does with equitable stroke control (ESC). ESC basically means that for the purposes of determining handicaps, your score on a given hole is capped at a certain level. You still write down what you made on the scorecard, but when you report it afterwards, it gets adjusted. Right now, my max score n most courses is an 8. So If I shoot 90 but on one hole I had a 9, the handicap formula uses ESC and records it as an 89.
Obviously in baseball, you wouldn't weight the adjustment, but you could still cap it.