The alternative would be a court-ordered re-vote of the run-off pursuant to its statutory rules, i.e. no votes by June 3rd Democrat ballot voters.
There is no precedent for doing what you suggest: limiting voters to June 24th voters, but excluding ineligible voters. That would indeed be disenfranchising voters.
The voters are bar-coded. Run a comparison of bar-codes in the dem primary and in the 6/24 primary. Discard the votes where the bar-codes match. Then, do the recount.
Again, this will require finding an honest judge in MS.