You can set up a complex rule to reprice against FBA Sellers exclusively.

Documentation on complex repricing rules setup: http://meanrepricer.com/Home/Documentation#conf_4
Complex repricing rule example: 

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In this example, the condition of your product is set to New and your competitor’s product condition is also set to New, and Mean Repricer will ignore the seller if the seller is not FBA ("FBA Merchants" Not Equal to True).