Well, no. Nobody was going to kill Jim or the baby. In fact Jim was captured while fleeing (by fiishermen, not soldiers under the command of William), and William later very carefully allowed him to escape, not wanting to create a martyr as with his father.
The baby had left the day before with his mother.
The Glorious Revolution was also not particularly violent, with under 100 dead on both sides. The major reason being that a great many Englishmen, often to their dishonor, switched sides. Including his two daughters. Not knowing whom among his remaining followers to trust, Jim lost his nerve and ran away, even though his remaining army still outnumbered the opposition.
I think you may both be missing the most important point about the succession, which is that it’s determined by Act of Parliament (the Act of Settlement), not by the wishes or whim of any particular monarch.
It began as a violent uprising. There was no way to know exactly how it would turn out. And fleeing the country, can hardly be called “stepping down”.
And, in fact, no English monarch has ever done anything like “stepping down”. There were some killed, some forced to abdicate and then promptly killed, and one that fled. Even the one minute Edw VIII was obliged to reside outside of England after he renounced the throne. So there is no historical precedent in England of a monarch giving up their throne to an heir and then pottering around the garden or taking up golf like a retired CEO. Again, it’s not a job.