I think your case is called "Dual Intent" and its a known scenario where I see no problem. As long as you have a existing valid work permit in Canada, which is the requirement or what qualifies your wife for SOWP, you can proceed to apply.
The PR application is not related to it.
The catch here is to convince "again" the Visa Officer that your wife will leave the date SOWP expires should they grant it...
This is of course considering that right now you are not PR yet.
But then if all goes well and your PR got approved in the near future, then no one needs to go back home or leave Canada anymore.
Good luck.
Check other threads, Here is an example same as your situation:
https://www.canadavisa.com/canada-i...our-pr-application-is-being-processed.461404/