I do see the argument for a rape metaphor, with the clones, with Troi, and with the Borg. They're all examples of people being violated.
I always did have a problem with Riker killing the clones. Regardless of how they were created, the clones had lives seperate of their own, even if they were still in development, they were damn close to being able to live their own lives, and they were innocent of the crimes done to Riker and Pulaski. It is an abortion metaphor, but it doesn't work well since the clones weren't in Riker and Pulaski's bodies. I wish there had been some real debate over the fates of the clones. There is often a tendency, especially in older sci fi, to treat clones as not really alive, not really human. I guess it's a thing with the era.
In a side note, I remember in the early 90s in Marvel Comics's series by John Byrne, Namor killed a bunch of clones of his dead wife who were said to have the intelligence of toddlers. They were innocent and harmless, although the man who created them had violated the corpse of Namor's wife. I think it was handled better though, as Namor was shown to be extremely grief striken at his wife being violated in her grave, and the other side of the issue was at least touched upon as Namor's cousin Namorita, who he was very close to, was revealed to be a clone of her mother, and this didn't change Namor's attitudes toward her. Namor was king of Atlantis, and cloning was illegal, so while he was in his legal right, I still found in morally appalling, as Namor essentially killed a bunch of toddlers, who were capable of maturing intellectually into normal adults in time. An interesting comparison to the less sophisticated way this issue was handled in TNG.
I also agree Pulaski seemed to be making a lot of decisions for those people in their relationships and family structures. I'd think a more detailed explanation of family planning and their reproductive options would've been more appropriate. Those people were intelligent enough to understand the option of artificall insemination if they wanted to pursue that. I'd think many of those people would have preferred using artifical insemination over having to sleep with people they didn't want to. I feel uncomfortable with this whole non-monogamy (and by this I mean sexual) issue being all but pushed on these people. If they chose it, fine, great, but it should be their choice. Without these people being given really informed choices the sexual component can feel kind of rape-y. In their situation, I think I might well feel that way.
These issues do make this a really creepy oogie feel bad episode.