You need to sign the passport forms as well. If you haven’t, and Passport Canada knows of your existence (through the birth certificate, for example), the application will be rejected.
You may have been instructed to go to the embassy to sign because they would be notarizing or authenticating your signature in English.
We have no idea why they wouldn’t let you access this service. If the passport application is rejected, we suggest that you print off the application yourself, sign it and then mail it to your wife for her to complete the rest of it and sign it as well.