The CBA doesn't address teams' franchise values at all. And I don't think the owners would ever agree to that, either.
What the CBA does do is share the hockey-related revenues between the owners and players. Basically, the players will get 50% of the revenues in any given year. But, because no one knows the actual revenues until the end of the year, but the players need to be played throughout, a portion of the player salaries is put into escrow. At the end of the year, a portion of the escrow funds will be returned to the teams, in order to ensure that the revenue sharing ends up at 50-50.
It really isn't a penalty as such. Even if we penalized teams for going over the cap, the player salary escrow would still be needed (see above).