You sound good, PYU,
It sounds like your mind kinda works the way mine does--it does a lot of "processing" in the background, but when we are ready to move, somehow it becomes very clear what we need to do.
It's important to act when that moment of clarity appears. It's like a window--it's only open for a brief period of time, and if we miss it, it might be awhile before it opens again.
I've lived with two alcoholics and with another person in an unhealthy relationship, and I'm a recovering alcoholic, myself (my own drinking really took off once I wasn't "taking care of" other people anymore). I had moments of clarity when it was time to take a breather from, and to finally walk away from, the relationships and, finally, from the alcohol.
I hope your wife chooses recovery, but you are doing absolutely the right thing for yourself and your son. Moreover, allowing your wife to stay would not be assisting her recovery at this point, so no guilt necessary on that score. She can choose to get well in a homeless shelter--that's what it takes for some people. Hopefully it won't get that far, but that's out of your control.
Stick around here, and hope the departure isn't any more painful than it has to be.