I'm a single applicant who applied in march this year. I've read here that as of early April it is now possible for families, even with children, to apply.
Now, I'm talking about applying for citizenship. You're on about applying for citizenship certificate as she is already a Canadian by birth, and that is a completely different ballgame. There are those who can apply online and those who can't. It all depends on the circumstances. If paper is the only route for you then so be it.
There is a questionnaire on the application info page you can fill out to find out if she can apply online or not.