Just to cklarify, you can use a multi-wire circuit with GFCI protection as long as you split the neutral where the GFCI's are fed.
That is, by using receptacles, not breakers (unless they're breakers in a sub-panel, in which case, the 'multi-wire circuit' is actually a feeder.)
In other words, the 'load' terminals must have separated neutrals; they can share a single neutral at the 'line' terminals.
I've done this where a jetted bathtub required two GFCI receptacles, for motor(s) and heater. I ran a 12-3 rather than two 12-2's.