No, those won't be logic output pins nor will they be running at 3.3MHz. That figure is for the logic (SPI bus) pins when toggling at that rate.
There's nothing you can do about the coupled length in the flex cable itself, anyway. No need to be any fancier on the PCB.
The best thing you can do is provide isolation between signals, by pouring ground around/under them. Hair-thin ground traces are a far bigger curse than where the charge pump traces are routed!
Tim