We're not a religious family, so his scrupulosity is more of the ethical/moral variety . . . . being the best, most honest, most upstanding person on the planet! I know . . . how many moms of teenage boys would complain about THAT?!?!
My mother (with teenagers of both sexes) would have, but when it came to ethics, we rarely saw eye-to-eye.

But anyway, I'm in a recycling ring, so I think I understand where your son is coming from, at least to an extent. Has he joined a ring?
But, seriously, it gets in the way at times, like when you're leaving a coffee shop and he's done with his drink and he's got a napkin that he didn't really use and you just want him to throw it in the garbage can that's 2 feet away, but he insists that he can't -- that that would be wasteful and harmful to the planet and he just HAS to put it in a recycling bin?!?! But you can't find a recycling bin in the vicinity, and you're late for an appointment?!?!
Why not just tell him to carry it out with him and deal with recycling later? I never use local public recycling bins myself because my town doesn't take recycling seriously, and no offense, but the setting you describe isn't the appropriate time or place for a mother to argue with her child about ethics, "green" or other.
Now, if, to use a more extreme example, he were stopping to pick up spilled hole punch dots when you were in a hurry to leave, I can see how that would be a problem. In that case, he needs to take a step back and view the big picture. Since the dots are not a potential ecohazard (or at least they shouldn't be, if they're made of paper) there should be no harm in leaving them. But again, a scenario like the coffee shop wouldn't be the appropriate place to talk about that. You need to discuss the matter with him in a relaxed, comfortable environment,
before he finds himself in that situation.
Or, he comes home from school with a folder stuffed with various slivers of scratch paper from this class and that class because he refuses to throw it away -- rather, it has to go into the recycling bin. These are his latest obsessions, and while they're full of good intention, they're paving his way to a personal he!! because he'll literally get so distracted by the thoughts that he'll forget to go to his next class, or he'll be 15 minutes late, etc.
If he carries an overstuffed folder at school and his academic life suffers from distraction, he probably needs organization. What kind of folder is this? Just an ordinary file folder with no seal, or is it like a notebook with a zipper? Would a zipper bag be better for holding the papers? He needs to keep his recycling papers separate from his work papers and not worry about them until school is finished for the day. If while working or on his way to his next class, he finds something on his hands that needs recycling, he should be able to put it away and resume working or going to class. Just as home troubles belong at home and work troubles at work, non-academic problems shouldn't occupy his mind or his hands during school hours.
Try to find out what's keeping his focus on paper in particular. Ask him what he believes to be the harmful effects of wasting paper. Perhaps he is concerned for the animals living in the trees harvested for paper. (But you may
not want to bring up a specific issue like that when talking to him, as it may inflame his guilt obsession. Let him be the one to explain.)
Or maybe he's just running on autopilot, performing mindlessly rather than mindfully. I must confess that even now when I handle recycling material, I sometimes find myself treating waste paper as if it were an ecohazard, simply because the concepts of waste and ecohazard have become so closely associated in my mind that I have to consciously remind myself that they aren't always one. It's the same with handwashing; if I don't consciously think about what I'm washing off my hands, I'm likely to wash the same way after eating as after cleaning a toilet. Like a lazy but resourceful computer operator, my brain just calls a "handwashing macro" for the same old routine.

(That could be more of an ADD thing.)
Also, has he voiced any concern about his privacy being compromised if he doesn't destroy his papers before they're recycled? (Again, you may
not want to mention this concern to him if you think it will make him more anxious.)