I agree that the studio has the right to destroy films. I do think that is unfortunate when they do.
I dont think, but I have no data so its pure speculation, that at least the majority of movies that get destroyed would not have much of a influence on the studio's reputation. Perhaps more for actors or directors.
On your second point I dont quite follow. In my post my suggestion is that after the studio has received its tax credits, the film would be available in the public domain for free.
Post tax break the movie has little utility for the movie.
This may require an adjustment in tax law. I am in no way well versed in that and I have little idea how it works.
The tax code could be amended for this scenario that the work being used for tax credit does not have to be destroyed.
(Again your 1st point is valid and a concern)