Why are the Terminal.app colors different from iTerm

Terminal.app has these colors hard-coded into it. Internal methods like +[NSColor(Terminal) vtRedColor] use hard-coded floating-point constants to set the colors.

As you noted, there are SIMBL plugins that can patch this but you've already noted their current limitations. SIMBL has been updated to support 64-bit applications, so you should contact the authors of the plugins to request that they rebuild them to support 64-bit. There's also another SIMBL plugin to consider.

The only other option for Terminal.app is to write a feature request at http://bugreport.apple.com and hope that somebody at Apple is enticed to add color customization to Terminal.app for Lion.

The problem is likely due to your vim settings rather than your terminal settings.

The color you mentioned is pretty close to color 224 (of 256 colors), so you might try looking in your vim colorscheme to see if that color is used in a ctermfg= declaration.

To test and see if I'm right you could try

:syn match Foo /foo/
:hi Foo ctermfg=red

If that turns the word foo red then you know your terminal's red is working properly and it will be an issue with your vim settings.