It doesn't seem like that's legal.

A production of RENT got shut down and fined because the director changed the ending...

PLUS

That's just not a good ending...

David, you left out that the strains of a sorrowful-turning-hopeful version of "Maybe" were heard from the orchestra beneath her tears. I like the ending. I think it really adds something to the show, takes away the sappiness of the original ending. I also sympathize with the reviewer's view that the director gave the show some edge. Aside from some book scenes and "We'd Like to Thank You, Herbert Hoover," the show really is played as a sort of saccharine, soporific fairy-tale that ignores the Depression almost completely, as we're caught up in Rooster, Lily, and Hannigan conspiring to get money and Annie being treated as the toast of the town by "Daddy" Warbucks.

As I recall correctly, living near Trinity Rep as I do, they did get bitch-slapped by the rights holders (I think Tom Meehan raised a stink, which is not surprising considering he won the Tony for the book and wouldn't be pleased about such a major change), and were forced to reinstate the original ending at some point in the run. Personally, I think that if it's a matter of staging that is not made a specific part of the script, Meehan should have accepted his royalty check and shut his mouth. That said, it's a fine line between allowing a new ending and allowing all sorts of other wholesale changes.

Legality depends, this was a Rep production (IE Professional) so I would imagine they had sought permission. That said it certainly would be illegal for an Amateur / community production. However I do agree that I don't like the ending.