It could work, but it's not without risks if you forget to turn it on again, and then start engine.
Air could be sucked in through weak seals, meaning bleed fuel system.
Not a good idea if you have just left pontoon.
You would have to be very diciplined about turning it on and off.
Has your injector pump got an electrically operated fuel shutoff, or is it cable?
If electric, why not rig a hidden on/off switch to that.