If you want to analyze a free body structure under the applied loads, then these applied loads must represents both the externally applied loads and the reactions and thus they have to be in equilibrium. Flexible spring still should be used to support the model to provide numerical stability for the solution, without providing any additional restraint.
This approach is somewhat different from traditional analysis when the structure is being analyzed under any set of applied loads, in which case the structure should be properly supported, so that the applied loads can be resisted by the reactions at the restrained supports.