That name format is not acceptable under Philippine law. Yes, there is a law for married names for Filipinas, and yes, the US embassy in Manila is very familiar with it. Options are: traditional format (like in your wife's passport), retain full maiden name only, or hyphenate maiden last name with husband's surname.
On the DS-260, make sure to use the name listed on your wife's PH passport, with her maiden last name as her new middle name. As mentioned above, regardless of the name listed on the I-130 (or the DS-260), the name on the visa will match whatever name is listed on the applicant's passport submitted at the interview. After US entry, the SSN card and the green card will list whatever name is on the immigrant visa.