Psychedelic_Rebel
If not fully satisfied with information from PETA, here are a few more sources:
http://www.hollywoodreporter.com/news/hobbit-animal-deaths-what-they-394826
http://www.deadline.com/2012/11/peter-jackson-again-denies-the-hobbit-animal-cruelty-claims-before-premiere/
http://www.eonline.com/news/366567/the-hobbit-controversy-animal-cruelty-allegations-cast-shadow-over-premiere-as-peter-jackson-again-denies-claims
Might I add: What better way to avoid unwanted controversy then to undermine the organization making these allegations? Play off the bad press generated by PETA by saying "Oh, it's just PETA up to what PETA does best".
Who knows for sure exactly what happened? PETA by nature will fight for animal rights as fiercely as ever, and Peter Jackson is going to defend this movie, because it is a source of billions of dollars to him.
So far, it seems as if one of these has glaringly obvious corrupt motives.
You are right that it is a logical fallacy to say that the claims of cruelty are wrong because people distrust what PETA has to say. Even untrustworthy sources (and I'm not saying that PETA is unreliable, I'm just making a point) may make valid points. But for the same reason, we cannot simply disregard Peter Jackson's (again, I'm not making any judgements here about PJ's reliability) statement because he stands to profit from the movie. Even though he has a vested interest, his claims may be accurate.
I think you make your best point saying, "Who knows for sure exactly what happened?"
Still, I find it incomprehensible to believe that anyone would intentionally harm animals in the production of a movie. Some animal injuries may have occurred, and clearly the AHA (American Humane Association) felt that any animal injuries were routine and accidental, otherwise they would not have signed off on the notice at the end of the movie that no animals were harmed.