It works as usual. Mold breaker affects the moves YOU use on a Pokemon with contrary, not the other way around.
If a move used by a Pokémon with Mold Breaker, Teravolt, or Turboblaze would change a stat stage of a Pokémon with Contrary, the change will not be inverted.
For example, if you use Rock Tomb on a contrary Serp with a Mold Breaker Excadrill, the Serps speed will decrease as usual since Mold Breaker allows it to use Excas moves as usual. But Serps own moves' effects wont be affected in any way.