If it's possible to have multiple "salary universes" active simultaneously, where each salary universe represents the locked in salaries at a certain date, that would be the best solution. But you'd need to incorporate the "universe" option into the salary search engine. Setting up a theme league, you'd now have the following options:
Salary Cap: 80, 100, 120, etc, custom
Salary Universe: As of 11/01, As of 11/15, As of 11/29, etc.
If this is not feasible, I like the idea of LOCKING in salaries once a team is entered into the league (open or theme league). This has the added bonus of incentivizing owners to get their teams entered quickly, before their favorite cookie goes up in price. If you are entered into a league and you notice that one or more of your players has gotten cheaper while you are waiting the league to fill, then yes, you could remove your team and re-enter using the lower salaries, but the odds are that other players' salaries went up.
I LOVE THAT YOU'RE FINALLY USING A DYNAMIC SALARY SCALE (which I proposed many years ago).