I assume whiskers cause a short circuit. Why can't the circuit board be coated with plastic, epoxy, non-conductive paint, or something to prevent the whiskers from causing a short?
You can't just spray anything on the board. Most coatings would separate from the board over time with due to thermal or mechanical stresses. There are many coatings that do work for this, but cause additional expense due to additional labor in finishing, and possibly design to make sure the components that need protected most can actually be coated.
Tin whiskers can break through conformal coating in some situations and the coating process does not always cover the entire surface evenly leaving thin areas or even entirely uncovered places in which whiskers can still form and escape. http://www.freelists.org/post/tinwhiskers/NASA-experiments-c...
Since the growth is caused my material stress, coating the solder with a hard plastic will shift the stress elsewhere, might cause another suite of problems.