The OP clearly has reasons for wanting to toggle the preference setting, and I don't think it's for us to tell him he shouldn't do it since we have no idea at all of what his workflow is, nor is that relevant to the question.
The original problem stated is that leaving Copy PDF to Clipboard slows down production, so he needs it off when doing copy/paste internally (and I think that may be symptomatic of some other problem), but he wants to turn it back on when he needs to paste into some other application. This is a preference choice, and it's a perfectly reasonable request to create a toggle for it.
I'm not a scripter, so I can't write the script, but I'm fairly confident it's a one-liner and that's all he's looking for.