Yeah, unfortunately not all ZAGS in Russia (or simply The Office of Registrar) register marriages between foreigners and russian citizens.
In this case,
@firewithin6667 go to another ZAGS in St. Petersburg. I don't know how about now but before it was Wedding palace #2 - tell that to you fiance, she knows what I am talking about. It was only one in St.Peter that does international marriage registration.
The process is correct but SHE CAN apply for the marriage ceremony/certificate WITHOUT you being present (so you can stay in Canada for 30 days while application is being processed). What do you need to do to make it is:
1. Make a copy of your Passport;
2. Get the Certificate of Marital Status to prove freedom to marry at your local Vital Statistics Agency (some provinces can be done via mail) - it may take 3 to 4 weeks;
3. She has to take a copy of marriage application at the ZAGS, scan and send it to you to fill out. (If you don't understand Russian, ask her to help but YOU have to sign it).
Take all
THREE of those I described above and
certify them in Notary Public and then
confirm this certification in the Ministry of Foreign affairs of Canada. After this part is done
send this bulk of papers to nearest
Embassy of Russia for legalization - it would take about 2 weeks max.
Once you get this paperload back, send it to her via mail (NOT email).
What SHE has to do is:
1. Translate it to Russian (if necessary )and Certify at the Notary Public;
2. Bring it to ZAGS and set the date of the ceremony.
After 30 days, you can get to St. Petersburg and conduct marriage.
Note: Make sure that you name in Passport and in Certificate of Marital Status is the same.
To make sure that this process still works, make her to go to ZAGS and ask if this would work with them.
If she doesn't understand what are you talking about, I translate these steps to Russian special for her.
But

If you ask me, consider all this butthert with translation, obtaining marriage letter from Consular, legalization of your passport and so on, I'd strongly recommend to do this process in Canada. Once you're married to each other on territory of Canada, you can fly back together and make unofficial bridal ceremony in Russia if her family insist so badly on that or whatever reason is.