Unless AFCI rules were amended out if you are still on 2011 NEC or earlier where you are, you don't run 12-3 to the first box for kitchen outlets anymore.
If using "feed thru" terminals of a GFCI receptacle - you can not supply MWBC wiring on load side of that GFCI.
If you have "three wire cable" running from outlet box to outlet box, you can put a GFCI receptacle in every box, but you can not have both 120 volt halves of the MWBC available at any individual duplex GFCI receptacle like you can with a standard receptacle.
I suppose you could run one GFCI load wire to the top of a standard duplex and the bottom of that duplex could be supplied via the load side of a second GFCI that is supplied from the other half of the MWBC. But you can not do this with only a 12-2 cable as the feed to the load side receptacle, sharing the neutral will not work with the GFCI's.
Otherwise a 2 pole GFCI breaker at the origin of the source gives you the same flexibility of which receptacle or half of receptacle is on which half of the MWBC there once was before GFCI protection was a requirement. It also is likley more expensive, and does leave user having to find the breaker should the GFCI trip, where the receptacle has the reset right at the outlet location. Feed through protected outlets can sometimes have you hunting for the GFCI though.