Dear Bo,
If the intra-cluster exchange is indeed >> the inter-cluster exchange (mimicing the Hund's coupling within one atom), this can be a good approximation.
A good test is to plot the magnon band structure with the 6 sites, and with the two effective clusters, to see if they matches.
If not, I think a way to do it is in the spirit of the downfolding procedure. That is given a 6x6 matrix with two 3x3 blocks and the inter-cluster blocks, construct a 2x2 matrix which matches the lowest energy spectrum. We can discuss if this is needed.
Best wishes,
HeXu