I have a CM 690 II Advanced, it's got a blue led switched fan in front.
There's 3wire output from the fan, to a 3pin motherboard connection in the standard layout. There's a second wire goes toa 2pin, goes to the switch in the case. The 12v hot is tapped at the motor point, goes through the switch, back to the leds and finally back to the ground.
So what you end up with is a 3pin DC fan, that responds exactly like any other 3pin DC fan, except it has a seperate 12v hot (same source as the fan motor) with a switch in-line for the leds.
That's how CM has been doing switchable leds like in a couple of the HAF cases.
The CM mega flow is just a DC fan with a molex connector that comes with a molex to 3pin adapter. There's no way to turn off the leds without affecting the fan operation.
The only way around that is to interrupt the 12v feed going to the first led on the fan itself (not the ground side) and after robbing the old fan of its connector and wire, putting the switch leg in series with the hots. Leave the ground leg seperate.
@Paperdoc
I'm not so sure about the 5v feeding the leds. Those are still standard 3pin fans, not proprietary. I'd suspect that there's a 5v/9v/12v switch, for low/med/high speeds at set voltages, so uses 5v-12v potentiometer. From my prospective, that picture is purely a fan control switch, the leds themselves having an off/on switch that's seperate. Nobody uses 5v leds in a 12v fan, and if they did, you'd still have a second lead for the leds, seperate from the 3pin fan power, going to a toggle switch.