I think it makes good sense. it's not the Federation's place to act as galactic police officer.
Also, how can species with different evolutionary tracts (and thus unique psychological traits) possess exact morals? Changelings, until Odo, had never hurt another. That's quite staggering, if this includes things such as basic assault and not only serious things as murder, rape, torture, etc. People in real life and in-universe view Klingons as brutal and bloodthirsty, well duh, it's how they evolved/are neurologically geared.
To some degree yes, but I think there's a line in the sand with extreme violations, such as genocide and slavery. Moral relativitism should be applied in some cross-cultural cases but it's got limits.
If there wasn't a civilian ban from interfering with prewarp planets, there'd be no prewarp planets left, because somebody would have traded warp technology to them for insane amounts of wealth the way Quark wanted to in Little Green Men.