YOu can still continue the process of petitioning for her.  Once the approval comes through from USCIS, it will be forwarded to the National Visa Center for the consular processing stage.  Since the consular interview will probably be done in Manila, as her place of residence, she would simply need to travel there for the interview once that is scheduled.  Once her visa is approved, she can then travel to the US.  In some instances, you may be able to change the consular interview to Kuala Lumpur, but if it is not a big deal for her to travel to Manila, that might be easier.