If you leave this will be considered as a completely new entry... And yes they probably may not be willing to grant you your work permit, even though nothing is really preventing them from doing so. (Talking from experience)
Considering you have a PR in progress, I'd suggest you wait. It shouldn't be too long now.
I understand this is painful.
The alternative could hurt your application for PR, get you in trouble, etc. or maybe work perfectly fine (if the WP can be asked at a POE). There is no way to know. It's up to the agent at the border.
Having been in this situation, I tried Niagara twice... to be rejected for no valid reasons and be treated like sh*t. I then requested a pre-approval letter for the WP, when to the US for a few days, and tried my luck at Pearson. It worked, but those were extremely painful and stressful days.