I assume you mean you are intending to change her name by using her marriage certificate?
I would just accept the citizenship certificate will be in her maiden name.
My understanding is you should be fine though in 'changing' her name - use the marriage certificate to update her eg Ontario docs, bank stuff, etc - and you can submit for the passport when citizenship certificate is received. Passport will be in new name (if you specify properly).
The citizenship cert can be changed
after it is received but it might take eg 18 mos. But it doesn't really matter because the (maiden name) citizenship certificate + marriage cert will be enough to show she-is-she and she-is-citizen.
https://www.canada.ca/en/immigratio.../services/canadian-passports/change-name.html
Personally I don't see any reason to wait until later in her case but if others can explain why