Still, I have trouble grasping how a phrase that literally alleges someone to be in an incestuous relationship with their mother can be a compliment. Perhaps it's about neutralizing the negative impact of the term -- taking something that used to be a rather hideous accusation and defanging it by reducing it to a meaningless quartet of syllables or even choosing to interpret it as praise. But it still sounds pretty strange to a literal-minded sort like myself. And when I hear people using it as an actual insult rather than a joking compliment, it still grates quite harshly on me.
(Since we seem to really be diving into this now...)
Linguistic drift is a pretty commonly attested phenomenon; even literal meanings change. "Maid" used to mean a girl of high class, and now it most often literally refers to a rather working class job. Your own example "golly" is another; most people have no idea where that comes from. Now my students use "thirsty" to mean "horny". A lot of people incorrectly ascribe word mutation like this exclusively to slang, but it isn't - "slang" is just a new use of language by a particular group of people, and that's how all language drift starts.
Denotational meaning is only valid when that meaning is intentionally implied; language isn't a set of external rules, it's a method of communication. Those men on the bus dropping "muhfuh"s so casually were absolutely not meaning, or even thinking about, incestuous sex. So, that isn't what the word means anymore. That's what word meaning is - what you mean when you say something. One can ponder the origins, and that can be surprising or interesting, but it has nothing to do with what people actually mean when they say it.
From a linguistics perspective swear words are interesting precisely because they so often lack any denotational meaning, and are purely connotation. The "mother fucking" in Kirsten's name expresses a set of connotations but tells us nothing whatsoever about any actions she personally did.
It's not even that odd that a positive phrase comes from an originally remarkably negative one. Lots of words do that. "Cool" originally was negative, implying distance and a lack of passion. It was reinterpreted as something desirable pretty quick. Hell, it isn't even that uncommon to hear people literally use the word "bad" to mean awesome. Or consider "that's shit" compared to "that's the shit".
Swearing indicates emphasis and power, both positive and negative; regardless of word origin, the effective meaning isn't literal at all. Analyzing swear words literally is missing their purpose.