I would send in the spousal sponsorship application before the refugee hearing. Why? Because if they decide she is not a refugee, and then right away she sends in a spousal sponsorship application, it will look like a marriage of convenience: it will look as if she only applied through the spousal category because the refugee claim failed.
I have asked my fiance to phone the CIC and ask them about what we should do, is this a good idea? I don't think it would hurt. I am working in a different Province(my job takes me away from home alot but not from Canada) which makes it a little harder for us to do this together.