Hi Iftikhar. Listen to the experts like Canuck78.
This is a tricky situation. I read somewhere here in the forum before about someone who was in the same situation like your wife. He Had the refugee travel document, his PR was completed but he travelled to the USA before receiving it. What happened was that he was not allowed to board the flight going back to Canada because he became PR when he was in the USA!!
So, if your wife will face the same thing, she will not be allowed to board the flight heading to Canada unless she applies for PRTD.
Like Canuck said, to avoid this all, it is better if she waits 2-3 weeks, receives her PR card then travels outside.