Yeah, no doubt that you have to be fast.  I use the same sequencer with the PitchFactor, and I don't know of any current way around what you're describing.  And – if you have an expression pedal thru connected – you're really screwed if you bump it and a knob while the sequencer is in Play mode.  Suddenly, you have more programmed parameters sequencing.

To be fair, I can't see how Eventide could anticipate users bombarding the expression pedal input like this.  For what it's worth, it becomes a little easier controlling program changes over MIDI.  I find myself not as dependent on the Eventide readout, and it prevents the on-the-fly programming mishaps.