This is a fundamental issue that has to be taken into consideration when designing your interactions. Our designers have a term for it, "the mic is always on." With that in mind, you need to consider ways to turn the mic on and off at appropriate times.
- Use a pinch to enable a control -- turning on the mic -- and release the pinch to release the control.
- Use one hand to "signal" that a control is active and the other hand to make the changes. For example, pinching or grabbing with one hand could allow the other hand to make unconstrained, expressive movements.
- If a foot pedal is a possibility, that could allow free, two-handed interaction when the pedal is down, for example.
- Leave yourself a free dimension. For example, you could use the x-y axis for setting controls, but leave the z-axis "free" so that you can withdraw your hands that way.
- Eventually, augmented reality will give you the ability to see and interact with artificial objects, but that's more future looking. (You can do it in VR now, but I assume that would be problematic in this case where you are primarily working with real things.
Now I don't know exactly how you are interfacing the Ableton with the Leap Motion software, hopefully it gives you the flexibility to achieve something like the above.