Actually, as Scotty's hand was frequently played by actors other than Doohan (especially when in closeup); if Pegg chops off his finger he will be violating canon. And if he doesn't chop off his finger, as Scoty as also been clearly seen with nine fingers, he will be violating canon.
I think the simplest solution is to give his hand a nondescript glove that leaves it vague as to how many fingers there are, sidestepping the contradiction in a Pavlovian sort of way.
But Scotty never wore gloves until he wore that radiation suit in TMP, so gloves on Scotty would also violate canon. (Wait -- didn't he wear a big black rubber glove so that he could short-circuit some equipment with a wrench in one episode? I guess he could wear that one canonically-established glove for the whole movie.)
What they should (nay, must) do is set up each shot to ensure that Pegg's right hand is simply strategically obscured whenever he's on screen. Based on the canonical record of Doohan's performance, Scotty simply had a right hand that nobody ever saw. They could even add a nice nod to the fans by having a line of dialogue where Kirk and Spock muse privately about never having seen all of Scotty's right hand at the same time. Sure, it would be a complete non sequitur for non-Trek folk in the audience, but the fans would love it! Box-office success would be guaranteed!
They could even make it a plot point...Scotty's finger is neither present nor missing, but exists in some sort of hyperspatial interphase, where its there-ness and not-there-ness exist simultaneously in some sort of quantum dactylic superposition. ....