Wow - that sucks and must be incredibly stressful. Good luck.Unfortunately your wife can't leave the country on a TRV/TRP. No Filipino allowed to leave the country as a tourist.
www.dfa.gov.ph/covid-19-advisories/26380-travel-advisory-outbound-travel-restrictions-by-philippine-government-on-filipino-travelers
We are in that situation ourselves, stuck in MNL now, BI wouldn't let my wife and son last Friday. Can't go to Canada, can't go home to Antique. We have written letters to BI, DFA and the CDN embassy trying for an exemption. I'll let you know if we make any progress.