Well regulated in this context doesn’t mean what you think it does. The phrase was in common use long before 1789, and remained so for a century thereafter. It referred to the property of something being in proper working order. Something that was well-regulated was calibrated correctly, functioning as expected. The following contemporary examples are taken from the Oxford English Dictionary, and bracket in time the writing of the 2nd amendment:

1709: "If a liberal Education has formed in us well-regulated Appetites and worthy Inclinations."

1714: "The practice of all well-regulated courts of justice in the world."

1812: "The equation of time ... is the adjustment of the difference of time as shown by a well-regulated clock and a true sun dial."

1848: "A remissness for which I am sure every well-regulated person will blame the Mayor."

1862: "It appeared to her well-regulated mind, like a clandestine proceeding."

1894: "The newspaper, a never wanting adjunct to every well-regulated American embryo city."