If you want, she can finish the contract with you and then go back to Philippines. But how can you trust her? She is working for you 3 months only. I experienced the same years ago. My maid worked for us about 7 months. I trust her and gave her a chance. Finally she resigned at the time when I needed her the most.
As I know, you can terminate her without notice because she is charged by the police with criminal offence. But you still need to provide the airticket. You'd better check with the labour department/immigration first.
She is charged by the police but not plead guilty yet. If you terminate her at this moment, I think you still need to give one month notice or in lieu of one month salary.