Unfortunately that means she will have to apply through Guatemala and if an interview is required, it will be held there and she will have to leave the US to attend it.
Make sure you are 100% honest about her history in the application. Her illegal status in the US will be forgiven by Canada. (Omitting this kind of history only leads to problems later.)
Also, hopefully you are aware that she will be banned from the US as soon as she leaves (likely for 10 years - but it depends on how long she has been illegal and how old she is). Is there any way you can legalize her status in the US before you move to Canada? That would be the better way to go if at all possible to avoid the ban and allow her to visit the US over the next 10 years. You should be able to adjust her status if you can show sufficient hardships.