An applicant does not have to be divorced (or formally annulled) to be eligible to be sponsored for permanent residence as a common-law partner but you won't be able to get married in Canada without her getting divorced. And it's my understanding that there is no divorce in the Philippines.
Also, your partner is in Canada illegally - so you have to proceed carefully with the PR process. You can apply to sponsor her for Permanent Residence, assuming you qualify as common-law partners (having co-habitated in a conjugal relationship for at least one continuous year) via an inland PR application while she's in Canada illegally - but that will not stop deportation proceedings if any have already been put in motion AND you can expect that it will take a couple of years for her to finally be approved. That's because of her illegal status - the application will be transferred for processing to your local CIC office and, depending on their backlog, it could be in excess of a year before they even look at it.
If you apply to sponsor her via an outland application, and an interview is required to verify your "genuine relationship", she will have to attend the interview in Manila and it is very likely she will not be re-admitted to Canada afterwards. However, that process, ultimately, takes less time than the inland process - and you have a right of appeal. Filing inland, you'd be giving up that right AND you'd be notifying them that she's in the country illegally - although, with a qualified relationship, they would likely not pursue deportation until they decide whether she's eligible for PR. That's the whole purpose of the inland process.
So, if things are going okay for her now - being here unable to work, etc. - you'd probably be better off filing inland, even though it will probably take a long time. However, Manila processes in 4-8 months (plus another month for CPC-Mississauga to assess your sponsorship before they transfer the ap overseas). If you have STRONG evidence of both your cohabitation AND your genuine relationship so that you could possibly avoid an interview about the relationship, it might be worth it to apply outland and just get the thing over and done with so she has valid status and you can get on with life. She wouldn't have to go back to the Philippines in order to be eligible to apply outland, and her staying in Canada (even illegally) would not factor into an outland assessment . . . she can use the Canadian address as her mailing address so she gets all communications from them while she's here, but she would need a family member's address in the Philippines to use as her residential address. It won't be "legal" for her to use a residential address in Canada - but they won't try to contact her in the Philippines.
A couple of things to consider: she will need criminal clearances from the Philippines, whether she applies inland or outland, and I don't know if you can get those without going there. She'll also need a medical - but that can be done in Canada. If she applies outland, she's going to have to get her passport to Manila when they request it - and it will have to be gotten back to her in Canada. If it's not legal to mail passports between Canada and Manila, she'll have to leave Canada to take it to them, and then "land" on her way back to Canada once her PR is approved.
