Somehow I don't imagine what may have been deleted will do any better of a job of explaining her character than what we have in the movie. I think that may end up being a flaw inherent to their interpretation of the character.
which is ultimately what makes her feel like she was just "thrown in there" which... infact she was.
The only thing she was needed for was the nanobot like bug that slowed wolverine's healing ability... her powers weren't needed, and there's nothing she added to the film other than a cool femme fatale. (which i might add, i would have loved to have seen her take on Mystique one day)
I stand by my assessment that the only reason she was added was 1 (she's been SS's body guard before, she was given powers because Marvel owns "Madame Hydra" where FOX owns "Viper", and they wanted another mutant in the film... (which i'm fine with, it'd be a bit odd that the US is littered with mutants, but Japan acts like they don't exist)
in all honesty i think Sunfire (Mariko's Cousin) probably would have been more of a natural flow than the forced Viper.
Maybe they should have said Viper is working for a terrorist organization, that is also behind the Yukuza. And she either wants wolverine's regeneration for herself, or for her organization.
but yeah, viper wasn't needed. anyone from the company could have put the nano-bot in him, and even if they didn't want to do the tech route... just poison him with special ancient ninja toxin that stops his healing factor till it passes. (similar to the story, when Storm, Wolvie and the gang's food is poisoned)