
the last thing you want is to get a deportation notice and be deported, and even worse the tax payer paying for it

, she could face a ban from coming to the uk for a while if that happens, even thou the bans are not mandatory for a spouse, but if she waits til the gov deports her, i would have thought she could well face a ban.
if she applies for her visa and its refused, i think she will be given 28 days to leave the country, she could then leave within that time and pay for her own flight, and apply for a spouse visa again(a chance she could still face a ban but not as long if she goes back b4 a notice is served)
but if she has heard nothing from the home office, it might be better she goes back to the phils asap and just apply for a new spouse visa, if she is not stopped on exit at the airport (small chance) the HO will not know she has overstayed, unless they can be bothered to check the stamp on when she arrived back in the phils

but a good chance she will not risk facing any ban.
thou she is better getting free legal advice b4 she does anything and makes a big mistake
she should contact someone like her local law centre and speak to a immigration solicitor for free and look at what options she has. but like i said b4 why didn't she apply for a visa b4 it expired, how long has it expired, etc need looking into
http://www.lawcentres.org.uk/lawcentres/