I'm sorry to hear that Jonny, and I can sympathise with you both.
It's a very tricky position to be simply because you will need to rely upon the reaction from UKBA.
I think you know already, but if you strongly request the return of the passport, then technically her application will be treated as abandoned.
However, similar to requests for emergency travel documents applications, if she can provide evidence of this emergency to UKBA along with an explanation then they may speed up the processing of her ILR application.
Please also indicate a planned travel date and be sure to state you do NOT wish the application to be abandoned.
Jonny, please take care to ensure that any 'travel documents' you actually end up using (whether passport or other document) will not only allow her out of UK but more importantly will allow her back in.
Take a look here for some extra UKBA information.
You must make contact asap
I don't think the Philippine Embassy can really help much, but may be worth a try just to know 'first-hand' so to speak.
