I'm going to run into the same situation with your spouse. My TRV is expiring in April 2017.(I'm also an inland applicant ) Despite the fact that it's highly recommended by most people here not to leave the country until the PR is granted, I'm planning to apply for my new TRV once I have got my new work permit anyway. I don't really see any reason why we can't re-enter Canada if we have the valid TRV ( Multiple Entry ). I get the concept of Inland app. that is meant for people who intend to stay in Canada during the application is being processed. But does not necessarily mean we are stuck here for like 2 years.. Plus, not that we are going to travel for months.
Aside of that, you should be able to just apply for the new TRV online, which should take less than 2 weeks to get it if you already obtain a work permit. Early of this year, I submitted my TRV online right after I got the work permit after graduation, and it took me only one week to get my TRV approved online, they then asked me to submit my passport for the sticker. So total around two weeks till I got my passport with the TRV sticker in it.