I always took it that the orca was trying to pull the cast off her leg because she was the one that was nice. Kinda like how Nolans ignorance started the chain of events, I feel the orca was trying to help her, and in his ignorance yanked her leg off.

The idea behind this film is that the orca wanted vengeance for the killing of his mate and child. The mythology of the film states that once an orca has been wronged it will go to great lengths to exact revenge if the person remains around the water. It does not care about what will be thought of its actions. Basically I think the whale's thinking falls along the lines of 'If you hadn't started this sh**, wouldn't have been no sh**'. The other crew members who got hurt were collateral damage as far as the whale was concerned.

he bit annies leg off to provoke Nolan "eye for an eye"
Like you also said though, Annie felt remorse for Nolan's actions. Even if the orca did spare Annie's life he crossed the line by biting her leg off and I do lose all sympathy for him afterward.

annie and dr. Bedford were the only two that showed remorse for what Nolan done that's why he spared both of them
he bit annies leg off to provoke Nolan "eye for an eye"
"Touchdoooooooooooooooooooooooooooooown Auburn"

You answered your own question: " Being permanently crippled could be considered a worse fate than death" especially for such a pretty young woman. The orca knew what he was doing by taking her leg off and sparing her life.