IMO, the Command key is one of the best features of a Mac.
But then I was on text-mode Linux (and before that, text-mode Unix) for many years. I would understand if someone used to Windows did not like it.
But control-c should not kill your session, only the currently running process. Control-d is what kills sessions. If you have no current foreground process the shell just starts a new input line. Still could be real bad obviously if a process is killed.
Don't get me wrong, I am not against specific boundaries for keeping people from doing potentially unwanted actions. But at some point, all the technical solutions to human errors are like sudo.
Even more, selecting text for copy, then clicking a mouse button for paste is a pretty much standard workflow. putty uses the right click for paste, while Konsole / Gnome Terminal / etc. use the middle click for that. Don't know about other Windows terminal emulators though. The other emulators that I tried pretty much had the same underwhelming behavior as cmd.exe.
The nice thing about Linux is that I can at least remap these keybindings. On OS X, it's literally impossible to do a perfect remapping of the keys (trust me. I've tried.)
Hopefully I've saved recently (or run the process inside GNU screen....).
You say you've tried to fix it.. Have you tried these?
In Terminal.app, find the setting for "don't close this window unless no commands are running", and select it.
Or, in System Prefs/Keyboard/mappings or somesuch, override Cmd-W in Terminal.app to a noop.
My experience was pretty hit or miss, and mostly I ended up with an mismash of semi-random keybindings which is sort of the opposite of what I was shooting for. On the Mac developers have done a remarkably good job of adhering to a consistent set of shortcuts (down to things like Command-, for preferences).
The other issue is that most apps don't make it straightforward to bulk re-assign keybindings from Control to Super, and last I checked it was impossible to turn off menu accelerators for Gtk+ based apps (e.g., Alt+F to bring up the file menu in Firefox).
Most of the time what I want is to map Command->Super and Option->Meta, and have Super replace Control in all GUI app keyboard shortcuts leaving Control available for command-line apps, in general.
That said, I've also ditched my Caps Lock key entirely and turned it into a second Control key. Control-A has never seemed difficult to me, at least with this arrangement, but I'm not a home row typist (or an Emacs user -- I just use the Emacs bindings in text boxes and terminals).
Otherwise this more or less mirrors my experience, although mine was ~7 years ago (so the Linux desktop environment was even less mature at the time). I haven't found a need to shop around for as many alternative applications. In particular, you can have Terminal.app when you pry it from my cold dead hands.