Yes, you can absolutely change your wife's last name during your application to sponsor your wife to Canada. All you have to do is to inform your Canadian immigration officer whoever is handling your case about the name changes. But first, your wife needs to change her last name on her passport and then submit the new passport with the new last name to Canadian Immigration in her country. She may need to submit a new police clearance report as well reflecting the new last name, to the Canadian Immigration.
It is actually a good practice to do all these before your wife lands in Canada because once she lands in Canada with the new name, from that point on, all her records will show her new last name. it saves her the hassle of having to run around and change her last name later. By changing her last name during the application won't cause any delay of the application process because this is a minor changes and the Canadian Immigration people understands this situation is quite common.