Your employee has a couple of choices:
1) Don't go until the PR card is in hand;
2) Fly to a US airport, drive across the border (some rental car companies allow one way into Canada, see thread in Avis forum), and then fly/bus/hitchhike to Ottawa;
3) If he has a US passport my experience has been that the airline doesn't ask for the PR card (once in Atlanta). This is risky because if they do ask your employee is SOL;
4) Fly to the business destination, then fly to a city with a Canadian consulate to get the 1 time waiver and pay the $50 fee.

I agree it's inexcuseable that the process takes 4-6 months to complete. I ran into this problem late last year when I found out by accident I required the PR card. I had to change my travel and drove across the border and then flew from US airports until I received the card.