Contrary to what some people feel that my present sigline may indicate, I rather like culture flipping. Probably because a majority of culture flips happen in my favor; I've had games where I've flipped over a dozen cities to my side.
As many properly point out, this is a game simulation--both of reality, and what we and the game designers imagine. Now since none of us has 6050 years of time, there has to be compression of events and abstractions. Some of those compressions/abstractions hardly get a second thought--population points, the time it takes to mine grasslands, etc.
Culture flipping ends up seeing a lot more second thoughts. I think this is because of a few factors: a culture flip as done in the game has extreme compression, instead of a longer and prolonged display of the conflict, a culture flip happens instantly and contrasts conspicuously with the more familiar military conquest which involves immediate tactics and long-term strategy. That makes it harder for the gameplayer to feel control, and I suspect it is even tougher on those gameplayers of warmongering inclinations. Whereas a builder mentality is more used to guiding production towards more abstract benefits, the warmonger prefers production that has upfront, almost tangible results, as tangible as one may get with digital simulation.
Now due to the nature of warmonger production, that player is more susceptible to adverse culture flips. It probably tends to feel like something that can't be controlled the way war and battle can be controlled. It is from this, I think, that much of the problems with culture flipping occur.
And perhaps it needs some sort of resolution, either a checkbox to disable culture flipping, or as suggested by the threadstarter, a method of resolution that isn't quite so compressed as the game engine currently performs it.