How on earth would withholding sex accomplish that? Anyway, I can’t think any reason that withholding sex would be constructive. I cannot imagine how deliberately choosing not to have sex in order to punish your partner could ever help to solve a problem. The one example you’ve given it happened to work out, but much more often that it will cause resentment, which is poisonous.
I’ll just trust you on that, but I hope you have items other than withholding sex and literal interpretation in your relationship toolbox. 
How about you propose to your girlfriend that the two of you do something special if the two of you can clean up the room? Doing something extra as a reward is very different, emotionally, from withholding something pleasant to punish her. Would you still think of that as manipulation?
Or how about sitting her down and telling her, “Listen, the messiness of your room is really bugging me. I realize that you don’t think it’s that big a deal, but it bothers me a lot more than it does you. We’re different people, and we have different tolerance levels for clutter. It’s getting to the point that it’s distracting me from enjoying the time I spend with you. I’d really like it if we could work together to clean things up.” Do you think that would be manipulative? Do you think that there are non-manipulative ways to get your message across? Were there steps less drastic than withholding sex that would convince her you were serious.
If you believe that she absolutely would not have ever cleaned her room without your doing something drastically manipulative withholding sex . . . well, that means she doesn’t have much respect for you and your feelings, doesn’t it?
How about the second example? Are there less manipulative ways to get her to say what’s bothering her? (As I’ve said, I think that what you’re doing is reasonable, but do you feel like it’s the right thing to do?)
It’s really all a matter of degree. It depends on how bad the problem is, and how severe the manipulation is, and what your personalities are like.
Are you a believer in the Golden Rule?
How would you feel if she told you something she wanted you to do, and she wouldn’t have sex until you did? Would you think that was a helpful thing for her to do? Would you think she was being fair? Would you feel that she was being respectful of you and your relationship?
It’s hard for me to imagine a hypothetical, but can you imagine a situation that parallels your literal interpretation thing? Or can you just put yourself in her place? How do you think she feels about it? Frustrated, possibly. But does she understand your side of it, or do you think she feels that you’re being unfair and manipulative?
Have you talked to her about this?