I use both a Mac laptop and a Mac desktop (but admittedly I don't use emacs). Both Ctrl+K and ⌘+K work the same, and the way I want them to. I write my code, then highlight, and hit Ctrl+K or ⌘+K. It indents the code and formats it as a code block, just as I would expect. Even works in chat. I never hit ⌘+K before entering any code (in fact I didn't even know that it would do anything if no text was highlighted, and only tried it because of this question).
I don't think I want this key combination to suddenly start deleting lines, and I doubt the entire audience of the entire Stack Exchange network wants to re-learn their key commands because you don't like the way it is now (and how it has worked for years). Perhaps you could find some type of add-in that intercepts your keystrokes, translates them, and re-submits.