Try sssPSX, you can use pad plugins with it that support rumble. Maybe they will have less performance impact.
You're using DirectX with constant motor for both large and small? Maybe your pad doesn't have two motors and the slowdown comes from the system trying to drive nonexistent hardware. Try setting large or small motor to none and see if that helps.
It could be a system problem - is your system's overall power drain near the limits of its power supply? If it is, the additional power needed to drive the rumble could be reducing power to your graphics card and therefore its speed. If this is the problem, you should see similar symptoms with PC games that support rumble. Do you?
Dan