Right, I think the key part to keep in mind is that color revolutions do tend to have an organic component to them. You have to have existing discontent or tensions that are exploited. The trick is to direct the discontent towards political goals that favor the west. This is done through NGOs, western media, grooming young people, and so on.

As you point out, a spontaneous uprising isn't going to have the necessary structures to create a functioning and independent government. When the dust settles, the existing power structures will reassert themselves, but under new leadership, one that's likely to be favorable to the west.