@RG, I think you kinda said it all. But here are a few thoughts:
I think as far as morality goes, almost all cultures have prohibitions/taboos on who one may/can/should kill, eat, or have intercourse with — but what those prohibitions are varies. In this sense, it depends on what you mean by “moral relativity”. If you mean, is there one absolute/universal system of moral coordinates, then no. But should there be a system, whether individual or collective? I think this is where it gets complicated. I think, collectively, there is always a morality. But within that, individual morality may vary — including outliers, who often end up being social outcasts.
Rumple’s claim seems to be that one protects one’s loved ones by “all means necessary.” This is the Machiavellian position, I guess. We’ve seen something similar with Snowing and Lily, but unlike Snowing, Rumple’s statement that he is dark — incorporating this into his identity — allows him to forego the sort of mental gymnastics we saw from Snow White where she had to literally dehumanize Maleficient’s child to justify her actions. But that’s not surprising — the Machiavellian position if actually a quite “honest” one.
For what it’s worth, I think Rumple is digging in his heels to counteract what he perceives as Belle’s intransigence, but they will need to find a middle-ground if this is to work. Belle’s a bit black/white on things. So when Rumple counters Belle’s (over-)statement that “darkness always wins” with “I’m sorry this happened to you” — this I think speaks more to something like “I’m sorry you had to stumble into the gray area in this particular way.”
There’s another theme that emerges out of much of this: does negative … lets call it “karma” balance out with positive “karma” (can they cancel each other out, for example), or are they entirely separate “bank accounts”, as it were? If someone does a good deed, does this good deed cancel out their bad deed?