Sadly, the original footage is, by all accounts, gone and was probably indeed burned to make room. From Robert L. Carringer's book The Magnificent Ambersons: A Reconstruction, which attempts to reconstruct Welles' vision:
As a protection against possible legal complications, the negative trims and outtakes were held for a time in [RKO's] vaults, but were eventually burned because of a shortage of storage space. (The leftover material from Hitchcock's Suspicion was destroyed at the same time, making it unlikely that this was a selective act of vindictiveness toward Welles.) The dupicate print sent to Welles in South America was deemed useless and was also destroyed. As a consequence, not even a frame of the extracted footage is known to survive.
The book uses the cutting continuity [a script detailing the shots that were filmed] in its attempt to reconstruct Welles' materpiece. It's the only complete record of the original footage. IMDb details some of the scenes that were cut:
It was 132 minutes long. It included an extended Ball sequence, an extended sequence of Jack and George in the kitchen [and] a completely different ending, as well as other cuts too numerous to mention. The original last part of the movie was (in order): George and Jack at the Rail Station, George's walk home and comeuppance, Fanny at the boiler, Bronson's office, Eugene and Lucy in the garden, George in accident, Eugene hears of accident, Eugene visits Fanny in the Boarding house.
A more detailed account of the lost footage can be found on Wikipedia here.