One approach would be to modify the way sub-stepping works so that instead of slicing the time into steps it uses a timebank. We didn’t do this in the engine because of the implications on blueprints where they rely on delta time to be representative of the real passage of time.
Using a timebank you tick at a constant rate every time, and you simply have frames where you do not tick at all or you tick multiple times. This will require some modification of the sub-stepping code though, so I wouldn’t recommend it unless you’ve tried the simple approach and it’s still not accurate enough.
This article better explains the details: http://gafferongames.com/game-physics/fix-your-timestep/