I don't think the megapixel count on the sensor is the result of a decision made a long time in the past. The sensor is a CCD from Kodak, which still makes very high resolution sensors at low megapixels[1]. I'm not familiar with the requirements of the sensor, but I'm sure that it was specifically selected. If NASA wanted more pixels, they were available.

[1] http://www.truesenseimaging.com/products/full-frame-ccd