This isn't a Dr. Evil plot, the boss isn't hiding anything from anyone, the boss simply believes other things are more important than a secure web site. "Web sites are cheap but a secure one is expensive" - is probably closer to the level of thought running through the boss' head. Programmers are not automatically "right" every time the say something needs doing. The boss in TFA probably sees the programmer as a loyal employee who's concerned about the quality of his work but is blowing the problem out of proportion.
It's a hard life lesson for geeks to learn that "correct" is not sufficient evidence to convince others to follow your lead in the real world. Of course you should cover your arse, but if that is your only motivation then your no better than the DR. Evil you describe in your post. If you turn the issue into a battle of wills, or a gotcha moment, then you will more than likely lose the argument and it will become more difficult to raise the subject in the future. Nobody benefits from that, least of all the programmer.
OTOH arseholes do exist and if you have one as a boss in a small to medium sized business there is little you can do about it other than to walk out. Don't think of it as quitting, think of it as sacking the boss.
Disclaimer: Developer with 20+yrs experience, computers are easy, people are difficult.