If you've read the book, then you'll remember that Kate and John met, fell in love, and conceived their first child before John became an alcoholic. You should also remember that back in the early 1900s (the setting of the book), divorce was practically unheard of, and people would rather live with the "secret" of alcoholism (or infidelity, or physical abuse, or incest, et cetera) than openly endure the shame of divorce.
That is why Kate and John stayed together.
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The mere fact that science may not yet adequately explain an object, event, or experience does not mean the immediate explanation should automatically default to a conspiratorial, extraterrestrial, paranormal, or supernatural cause.