Hello John,
This is a common question we get here at the forum, but good old Ian has hit the nail on the head, he tells it as it is, Bite the bullet, if you intend to live together as man and wife in the future, suggest your girlfriend leaves the UK now, although I suspect if she has overstayed, its by a good margin.
People tend to ask this question long after the horse has bolted through the gate, the problems now for like minded ones, is that they can be barred from re-applying to enter the United Kingdom for up to 10 years, although that is related to lying or supplying false or fraudulent information to UKvisas.
I concur with Iain, because UK Border Force at present has no exit visa system, she could leave the UK, without having an exit stamp placed in her passport, however, the problem is always one of Philippine Immigration, who unfortunately stamp the passports of inward bound Filipino's.
That is where your problem is, hopefully, if they don't stamp it, I understand it can be arranged locally for an express fee, (you will have to find this out through other Filipinos) then there is no reason why your girl cannot legitimately apply for a fiancee visa, to come to UK, on the basis of her relationship with you in UK whilst working here,
but you suggest she has put much into the country and or the economy, why has she overstayed ?
If she is on a work permit, has not the permit been renewed ? if not why not ? how long has she been here in the UK, is she not close to indefinite leave to remain as an OFW
You seemed to have left out some important information.
Unless we have the full picture, its very difficult to give an accurate advice, since you have left so much out, suggest Iain's advice is correct.