I remain concerned that in a moment of cult-inspired madness she may try and take my son with her to the Philippines to remove my Satanic influence
Philippines is not an easy country to live in, so I find her comments that she may move back there for a quiet life unlikely. She may leave you for a quiet life if you do not ease up on her, but going back it less likely. Then again, I don't know what the situation is with her and money, or residency status. In Australia, after 2 years they can get permanent residency with ease, and easily find a job, or support themselves off the government and child support, so few ever choose to return to Philippines.
Why are you so worried about what she believes? For the sake of your son, the best thing is to make sure you educate him so that he does not fall for the cult. But pushing her away due to her religion, one that she had before she met you, is putting your relationship with your son at risk.
Helping Someone Leave Jehovah's Witnesses provides advice on helping your wife. Until you fully know why she is a JW, why she believes it is the truth, and how much faith she has in it, what you say to her could do more damage than good.