A good start would be using the proper atmosphere when heating the steel. You can also remove the decarburized outer surfaces if you find it too difficult to control during heat treat. As for the acceptable level of decarburization in your part, that is entirely up to you. Section 3.5.1 of AMS 2759/1 provides guidance for accept/reject criteria of decarburization in heat treated alloy steels with a TS below 220ksi.