Allow the Terminal.app to pass command key  based keystrokes to terminal programs
I have similar desires to yours. I solved it using a system-level modifier-key re-bind.

(Of course, this is a mess; but I find it worth it to maintain my MacVim-trained hybrid of OS-wide controls (save, new, copy, paste) within command-line vims.)

Here's how I did it:


Install Karabiner, which is a very, very powerful program (and an essential part of any poweruser's / programmer's OS X installation, IMHO)
Enable “Command_L to Control_L (only in Terminal)”:


Map ⌃-prefixed controls matching whichever MacVim commands you're most used-to in command-line vim. For instance, to support ⌘S,

noremap  &lt;silent&gt; &lt;C-S&gt;    :update&lt;CR&gt;
vnoremap &lt;silent&gt; &lt;C-S&gt;    &lt;C-C&gt;:update&lt;CR&gt;
inoremap &lt;silent&gt; &lt;C-S&gt;    &lt;C-O&gt;:update&lt;CR&gt;

Restore expected ⌘-sequences for Terminal.app itself, by special-casing them in System Preferences. For instance, if you want ⌘N to still control Terminal tabs, instead of mapping it to vim files, try:



Now, anything you don't add in this list, will be passed through verbatim to command-line vim (and, of course, any other command-line program you use.)




Caveats

This approach has several further subtle downsides, that I want to hilight for anyone considering taking it (as I do):


⌘␣ will no longer map to the system-wide Spotlight. (I've an open issue on Karabiner, and will come back here once I have a stopgap solution.)
For reasons I can't ascertain, even with the ⌃W exclusions set up in System Preferences, the tab-closing behaviour of Terminal.app changes with this setup: ⌘W will close individual tabs in a window; but if the current tab is the last tab, it will not close the window. Instead, it has no effect. I've had to re-train myself to use ⇧⌘W to close the window if there's only one tab left.
If you've trained yourself to use ⌃V in MacVim to do block-wise selection, then you'll have to re-train yourself to use the alternative, ⌃Q (or, now, ⌘Q). Additionally, you'll have to add stty -ixon in your shell's startup-script, as ⌃Q is consumed by default to preform an archaic shell-control function (one with no modern usage.)




Alternative ⌘W behaviour

In addition to the above, I decided to further override ⌘W as a universal ‘close this’ key, applicable to multiple applications.

Instead of mapping ⌘W to ‘Close Tab,’ as above; I personally map that to ⇧⌘W (to retain “immediately close this tab” semantics.) Then, in any given program, I map ⌃W to some sort of close-save-quit functionality.

For instance, in my .vimrc:

noremap  &lt;C-W&gt;    :confirm quit&lt;CR&gt;
vnoremap &lt;C-W&gt;    &lt;C-C&gt;:confirm quit&lt;CR&gt;
inoremap &lt;C-W&gt;    &lt;C-O&gt;:confirm quit&lt;CR&gt;


… or my .zshrc:

function close_tab { exit }
zle -N close_tab_widget close_tab
bindkey           '' close_tab_widget
bindkey -M vicmd  '' close_tab_widget


With those two snippets in place, and your Terminal configured to ‘Close if shell exits cleanly,’ a series of ⌘Ws will first quit vim, and then close the shell entirely.

In addition, now additional on-exit functionality of programs can be preserved: for instance, vim will ask before quitting if files are unsaved (just like MacVim); and zsh will ask before quitting if there are background jobs.



Postscript: Not directly related to your question; but you should also check out ‘Ubiquitous Vim Mode’ in Karabiner. It's “a bit much” for me to use everyday, but it's a very cool idea, and surprisingly-well implemented.