How do I close an OS X application from the command line using a alias defined in my .bash_profile?

Use a function instead:

function quit {
osascript <<EOF
  tell application "$*" to quit
EOF
}

Aliases can't have parameters. Aliases do a strict text substitution, where 'parameters' would kind of end up at the end.

I'd do a function, which can have parameters.

function quit
{
    if [ $# -ne 0 ]; then
        echo "usage: quit _appname_" >&2
        return
    fi
echo | osascript <<EOF
tell application "$1"
  quit
end tell
EOF
}

Sorry, but I can't test this and verify today (no Mac), but the idea would work as a function.