An age-old question is, "How do I make it sound the way I want it without actually having the skills to make it sound that way?" The answer continues to be, in many cases, "Hire someone who can do what you want done." See, e.g., Glen Campbell's tenure with the Beach Boys, through Steely Dan's roster of hired-gun studio guitar guys, and on and on. Another answer is "fool around with it in the studio." Most recently that latter answer has been more specifically "apply a Pro-tools plugin until the swelling goes down" in a fair number of cases. But some version of this answer has been applied for as long as it's been possible to edit recorded music. That Lester Polsfuss - what a fraud!
But seriously:
Where in the world can you get a sound like "Bohemian Rhapsody" except in the studio? The answer is: nowhere. A lot of more recently recorded music does not have the pedigree (to some of us older guys) that Queen did, but it's really deja vu all over again.
So with respect to using autotune on a guitar (or a singer, or what have you, or even using a drum machine):
The question is not really: Is this a legitimate thing to do to a guitar part?
The question is: Do I accept this as music, and more broadly, as art?
On the one hand, sure it's art - it's just art you don't like. On the other - it's a manufactured product that perhaps exhibits less of the individual technical skill and/or idiosyncracies that make music more "art-y" by your own criteria, and so it's bogus and not to be granted artistic legitimacy in your own belief-system.
EIther way - the future is here, son. If you don't like what you hear, make a noise you like better, or change the station. Complaining about it is like complaining about the weather, or politics - it doesn't do a lick of good.
Opinions expressed here are not necessarily the views of the management of this station, blah blah blah, add water, makes its own sauce, so you don't forget, call before midnight tonight!
Bagman