I know that breaking promises can make players quit and hurt your reputation, and that revoking scholarships can also hurt reputation.

That's why I decided to keep the Junior PG signed by a previous coach who I just don't want running my offense. He's #3 on the depth chart behind a Senior and my newly recruited freshman. I just recieved notification that the Junior isn't happy with his playing time, though I obviously never promised him minutes. If I continue down this road and he quits would it hurt my rep? I would have revoked his scholarship myself if it wouldn't have hurt my reputation, so I want him to leave after this year, but only if i'll stay at A+ rep.

This won't hurt your rep at all. Even if you did sign him, it will only hurt your rep IF you promised him minutes, and he leaves because you did not honor the promise. However, the odds of him leaving, no matter how little he plays, and how much his WE drops, are fairly low. Possibly a better option (than the one you chose) was to cut the player before signings. It would not have hurt your rep (since you did not sign him), and you would've gotten the additional spot of recruiting money for next season. Do note that if you cut such a player, there is a very small chance another player will leave with him (in theory because he is "upset" his buddy got cut). The first you'd hear of such an outcome is when he leaves (there will be no warning or chance to undue the cut).