This is quite a disturbing topic. I hope nobody takes this personally.
If the 'power' operates primarily on pheromone cues then in reality it's almost impossible for the target to realize that anything had happened unless the behavioral effect is contrary to a firmly held aversion to the act. Causing a dedicated pacifist to commit unprovoked violence against a stranger for instance. If the act does not cause a significant inner conflict, and if it is not 100% clear that the target was ordered into the act against what would normally be their will, then there is very little chance that the target/victim would be aware that they were manipulated.
Even if the act itself was normally abhorrent to the target there's an extremely good chance that they will internalize the responsibility for the act. Depending on the nature of the act they could suffer significant mental anguish and potentially radical self-image alteration leading to personality change or even psychosis. In short, the inner conflict could drive them insane.
If the act itself was something the person might choose to do under different circumstances then no such conflict should arise. If the target might have chosen to have sex with your protagonist without the influence of the power then they will almost certainly never realize that they did so because of external influence.
In this case the only chance the protagonist has of being caught out is if multiple targets confer on the strangeness of their behavior. A room full of court officials being manipulated to break the law for the protagonist who subsequently review the case and start asking questions would be quite likely to figure this out for instance. Video evidence that shows abrupt change in behavior would also help others to figure it out.
The same might be true of a telepathic influence operating on a subconscious level. As long as the target isn't confronted with clear evidence of manipulation they will continue to believe that it was their own choice to take those actions.
The only way they could work it out for themselves is if the power operates to supplant the ego of the target, leaving them fully aware during the activity that they are not in control of their own actions. Imagine being trapped in your own head for weeks while a stranger - one who is exactly like you in most respects but who is definitely not you - controls your every waking moment. You know what is happening but you can't do anything about it. You can't even look away from whatever it is you're doing because you have no volitional control over anything. All you can do is sit in the prison that is your body and watch. Over time as the control wears off the victim's own conscious mind would reassert control... and probably suffer complete mental collapse.
Either way is pretty terrible, but I think that being aware that you are acting against your own wishes and being unable to do anything about it would be by far the worst situation. Possibly the worst thing I can imagine happening to me, certainly. If it didn't break me it would set me on a path of vengeance against your protagonist.
Assuming that the "I know I'm being controlled" variant goes too far, there are a couple of other quite nasty social side effects that could happen once your protagonist's power becomes known.
As soon as anyone finds out that there's a mesmeric individual in their community, regardless of whether or not they know who it is, they will start to question all of their own past decisions and actions. For some this won't be a big deal, but for many it would be pretty damaging. A lot of people would start to lose confidence in the accuracy of their self image, which is a fundamental part of yourself that most people don't ever question. Some would go crazy without ever encountering the protagonist simply by knowing that such a thing is possible.
On the other hand, there will inevitably be those who will use the existence of such an ability to justify their own actions. "You don't understand, your honor, I was being controlled by that Puppeteer" will become the number one defense in court. And unless there's some way to prove them wrong... what do you do?
Eventually the society in which such an individual existed would be forced to destroy them or face destruction itself. The only alternative is to find a way to stop the effect, and there aren't many people who would be willing to take the chance that their society would survive long enough to get the job done.
What does all of this mean for your protagonist?
From the question it seems that they have a moral code that makes them at least try to do the "right" thing. In this case the most moral action I can think of (apart from suicide) would be complete isolation and study. Alerting the authorities would result in the protagonist being either locked away for study or terminated for the good of the society. Probably some agency or other would try to use the ability, with appropriate safeguards to prevent it being used on the agency itself.
Let's say the CIA decides to take your poor puppeteer and use their powers to further the Agency's interests. Nobody could ever resist interrogation, lie to the Agency or go against the Agency's wishes if they were controlled like this. A medium-range anesthetic dart or a room full of knock-out gas to bring the protagonist down, then implant a radio-controlled poison capsule to ensure compliance. Of course the people in control of the activator for this would have to be kept clear of the asset, but that's minor stuff that a simple telepresence rig can cover. The CIA has been doing shady crap for long enough to figure this out in a matter of seconds.
So yeah, run and hide. Because if they find you, you're worse than dead. They'll study how it works, try to replicate it, then either dispose of you when they figure it out or force you to do their dirty work for the rest of your life.
And now, the bit that most people probably don't want to hear...
Consent is irrelevant here.
Not because it doesn't matter, not because anyone is justified in proceeding without it, but because under these conditions consent cannot exist.
Consent is necessarily either ephemeral or meaningless. Free consent requires the freedom to withdraw consent at any time, immediately terminating the activity consented to. (Yes, even CNC - that's why people invented safe words.) Your protagonist's sexual partners don't have that freedom, so by definition they cannot give consent for the activity.
If they realize after the fact then they are completely justified in retroactively withdrawing consent; a legalism that here simply means recognition of the fact that any consent given was never in fact valid due to the coercion. And you know what we call non-consensual sex, right? Right.
Even if they manage to gain some control over the power they will probably never be able to know for certain that consent was given without their subconscious "accidentally" nudging the other person.
As a moral dilemma, this one is a doozy. If they aren't fundamentally immoral then the only realistic outcomes I can see from this are complete isolation or suicide.
For an amoral person however... well, let's just say "power corrupts" and leave it at that.