As much as a game allowing multiple "classes" of rogues would be, and as much as a game without the objective of "kill every ************ in the room" the whole time would be refreshing, I think the game shouldn't force the players to take the pacifist route, either by having guards so overpowered that ANY fight is suicidal, or arbitrarily failing the mission for making a mistake because "The enemy suspects foul play, so they're completely tossing their game plan". Instead, it should be that stealthier operations don't escalate the difficulty of the next level (at least, any more than the escalation should be), but sloppier runs get more attention, and more security measures are used for the next level.
For example, say you need to find information on a drug syndicate, or need to steal a diamond from a museum. If you kill one guard, it will raise everybody to alert status (and they'll stay on alert status for the whole level), but it won't matter much in the next level if you can complete your objective without killing anybody else, or getting caught in the process - not to be cynical, but a nine-to-five schmuck getting iced won't have cops and/or gangsters swarming as much, say, realizing you stole whatever it is you stole. Butchering everybody you see will have all the remaining guards freak the fuck out, shooting first and asking questions when you're dead, bringing in reinforcements from outside the level (making escape all the more harder), and will even have following levels even MORE heavily guarded and on alert status before you even get there (even if you "leave no witnesses", everybody will be freaking the fuck out over the mass murders).
Again, killing shouldn't be discouraged by having the act of killing rendered impossible, and getting caught with "stealing" information shouldn't result in failing the next level because the bad guys completely changed their plans by one bit of data being compromised - it should result in levels going from a handful of guards not expecting any trouble to CRAWLING with guards who are on high alert for the whole level.
Incidentally, I think the plot should either be of a thief (or a gang of thieves) out to rob a bunch of rich fucks blind (a la the Thief series) or a person (or a lot of people) out to get revenge on the people who screwed them over, and left them for dead. The first story will naturally have increased difficulty curves as you go stealing more and more precious items, but will increase the difficulty curve enormously if you kill hundreds of people in the process (and will brand you as a mass-murdering psychopath rather than a rascally thief, to hammer home how badly you've crossed the line). The other allows a fresh take on the "person out for payback" plot by giving the option to go on a roaring rampage of revenge WITHOUT needing to kill anybody. The closest things I can use to describe these options are the "pacifist" eliminations from Dishonered (getting a pair of slave drivers enslaved in their own mines, getting an aristocratic ***** spirited off by a stalker, etc.), or the plot for The Count Of Monte Cristo - the Count outright states that killing his enemies would have been easy, but truly getting revenge by completely humiliating and destroying their lives - that's gonna take a bit of hard work. It should be easy to give objectives for these "pacifist eliminations" - if they're criminals, gather evidence for the police to arrest them, and imprison them for the rest of their lives. If it's not possible to arrest them, find a way to screw them over in a way that death would be a mercy for them. And if you do that by not harming a hair on the hair of their guards (therefore not becoming as much a monster as your real targets) - so much the better.
The only cherry on top is to give special cutscenes for taking the pacifist route, at least for taking the most high-profile jobs: Yahtzee once said in one of his videos that he always wanted to keep the guards alive because he could imagine them stomping on their hats in rage when they see they've been duped. In order to make non-violence as cathartic as immediately "killing every ************ in the room", there should be some cutscenes where everybody finds out what you did, and promptly flips the fuck out, but you're already laughing your way to the bank, you handsome rogue you!
