The concept of a telepath invading a person's mind and being equivalent to rape is a good one. It should not have been actual images of rape or even sex.
I could have gone something like this:
The villain has a good one-on-one conversation with Troi, but when it gets too personal, Troi is uncomfortable and leaves. It needs to be specific, such as describing a memorable date with Riker, but stopping when they enter the bedroom. We then see the villain talking to his father about his intriguing conversation with Troi, perhaps remarking that human dating rituals are very peculiar. Later, Troi then has a dream about that event but it continues into the bedroom. It should not be rape, but something should feel "off". For example, when she runs her hand through Riker's hair, it is long blonde hair, which freaks her out and she passes out. Both the villain and his father have the same long blonde hair (or maybe they both have ridges on their hands and that freaks out Troi when she clasps Riker's hands), so we don't know, which one invaded her thoughts.
We then see both the villain and his father have a conversation with Beverly about something that intrigues both of them, but Beverly gets uncomfortable and ends the conversation. Again, Beverly has a dream that replays the end of that scene and continues beyond where Beverly wanted to stop. Something clues us in to the fact that the other character is one of the aliens but it is again we can't tell which one.
Picard and Riker then talk to the aliens. The villain can see that Riker is very agitated, asking tough questions but is tempered by Picard, who says "Ok, we will discuss this." We see Picard meet with Riker and agree with his plan to contact their alien home world (or something). The villain is concerned and wants to know what was said, so he invades Riker's mind to learn what was said in the meeting, but we see the villain's father take the place of Picard and argue against Riker's plan, but before Riker collapses, we see the alien mother or father walk in on the villain and disrupt the session, so Riker is confused and groggy but doesn't pass out. He remembers seeing the father's face, so he comes on even stronger to accuse the father, who tries do defend himself, but is placed in the brig. The audience knows that he is wrongly accused but how will they prove it?
Soon after, Geordie provides the evidence that the other events could only have been caused by the son. So now we have a dilemma. Could both the father and son be doing this? The son on the other worlds and the father on Enterprise? Is it possible for the aliens to implant thoughts, a false image? When they acknowledge that yes, they can implant thoughts, their entire body of work is questioned. The villain, as much as he is frustrated by his father, does not want to see all of his father's work ruined, so he confesses. Can we believe the confession or is he protecting his father? They then look at the times that these events happened and prove that it could only be the son.
So, it is possible to show the mental violation without showing sexual rape or having the audience wonder if Riker actually raped Troi, or whether that was only the villain. And the audience doesn't need to know too early who the true villain is.
Another possibility is to have a series of more subtle, minor invasions that the characters can talk about "I had dreamt about x but it felt weird, different, but I can't explain how." this builds to them passing out.
