Philip Gossett in his book Divas and Scholars talks quite a bit about the war between tradition and scholarship or the conflict between what we are used to hearing vs what the original sources say. He cites a lot of examples.
The Il Trovatore example is interesting. We will posit that Jean de Reszke or one of his imitators needed a high note to show off his pushed up chest high c, and the rest was history. So should every tenor be required to do a high c there in order to remain competitive, even though Verdi didn't write it? Important critics at important newspapers like La Stampa or the New York Times want to hear the opera exactly as they have already heard it.
If Richard Bonynge decides to spare his wife Joan Sutherland a death scene, perish the thought she should have to get down on the floor, and changes the ending to Semiramide to one where Arsace kills the bass Assur instead, should future producers be required to defend changing it back to the original plot? The film with Montserrat Caballe uses the original ending.
If Cecilia Bartoli decides to do different arias in Le Nozze di Figaro, even though she can fully justify the changes all the way back to Mozart himself, should we continue to make an endless fit over it, effectively driving a major artist out of New York?
When crunch time comes, decisions are made. There are two pieces to the argument: 1. What should the score contain? 2. What should the performance do? Controversy is the mothers milk of opera, as I have written elsewhere, and we should not be put off by it.
First question, what should the score contain? It is not possible to justify issuing printed scores and published materials that do not reflect the highest scholarship. If the composer wrote alternate versions, all should be included. Any other answer is nonsense.
Second question, what should the performance do? Opera is still show business. If you can make it work in the theater, you can do it.