It can be done by 'late-registering' the births and putting 'father unknown' on the new birth certificates, but only if the births haven't yet been registered at the NSO in Manila (quite likely). This is a desperate measure, but I know it has worked.
You would then be depriving a father of his children. Hmm.
Other than that, without the father's written permission I think your chances of taking the children out of the country are zero.
Now that I'm searching for a new Filipina girlfriend, I automatically reject any with children. Harsh, but avoids this kind of problem. Even that can be risky, as so many say that they have no kids, but in reality DO.