I hope I don't misunderstand, please put me right if I do.
But if you mean can you go to the Philippines marry your lady and then she applies for a settlement visa, then the simple answer is yes.
It's most unlikely that UKBA will refuse based on her previous overstay.
Without knowing the full details behind her UK exit and what the exit conditions were, it's difficult to say whether she faces issues during 2 years, 5 years or 10 years. Those exit details have still not been explained.
The other possibility that may be worth a try is that your lady could put in an application for a Fiance(e) visa. This is a settlement visa. You both would have some months together to decide if marriage is a good decision or not (based on the fact that your still undecided). The Fiance(e) visa is issued for 6 months stay.
Recently, the Fiance(e) route has proven to require some additional evidence that the relationship is genuine and that the intention is actually to get married.
Yet another possibility, and a much cheaper one, is to consider having your lady apply for a Marriage Visit Visa. This visa is essentially a visit visa, valid for 6 months, but with the specific objective of getting married in UK and then returning to the home country with a view to apply for settlement.
Yes, I know it's a form of visit visa and stand a good chance to be refused based on her previous overstay, but it only costs £78, so maybe worth that risk. Certainly wouldn't impact the subsequent settlement visa application.
Maybe in some way in could strengthen it. (ever the optimist eh)
The final opportunity may not be at all appropriate, I just don't know, but have you reviewed the issues around the EEA route?
Just as a first step do some search here on the forum for EEA route and determine if it's even worth considering.
Just trying to help by throwing some ideas around.
Food for thought.