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In general it's better to use the camera's native API to get the data and then use openCV to convert the returned data into an image, openCV contains a number of Bayer pattern ->BGR routines specifically for that. The VideoCapture interface is convenient for testing, because it can seemlessly read from a camera or a file - but it's not really suitable for high-speed real-time vision.
That being said, it depends on the camera. For example, OpenCV has a backend for the Allied Vision GigE camera's, and it has some other backends, but I am not aware of a universal one. I am unsure about the GenIcam ...
