Conference points mean making the major or not and seeding so they definitely mean a lot in the grand scheme.

A 100 point deduction to an 'A' team means they don't make the major. A 100 point deduction to a Major team could mean they are the 4 or 5 seed instead of the 1 seed for the major. Who does that hurt? It hurts the teams that have to play the #4 seed when the 4 is actually a 1 seed caliber team.

Points deductions have never been a viable solution.

Giving zero points for a tournament could be a viable solution in some instances but subtracting points from the teams total earned for the year is usually devastating and very hard to enforce.