How to make Rsync copy alias files?
Rsync can't look into the content of Alias files which would be needed to convert them. So if you want to have your backup be useable as is (without restoring it to the orignal drive) you will have to replace the Aliases with symlinks. 

There is a solution for this on MacOSXHints.com. It needs to be run on your original disk (not on the backup), I would also recommend to test it on some sample directories first.

#!/bin/sh
if [ $# -eq 0 ]; then
    echo "Usage: alias2ln alias1 alias2 alias3..."
    echo "  where alias1, alias2, etc are alias files."
    echo "  Each alias file will be converted into a symlink."
fi

while [ $# -gt 0 ]; do
    if [ -f "$1" -a ! -L "$1" ]; then
        item_name=`basename "$1"`
        item_parent=`dirname "$1"`
        item_parent="`cd \"${item_parent}\" 2&gt;/dev/null &amp;&amp; pwd || echo \"${item_parent}\"`"
        item_path="${item_parent}/${item_name}"

        linksource=`osascript&lt;&lt;EOS
tell app "Finder"
set theItem to (POSIX file "${item_path}") as alias
if the kind of theItem is "alias" then
get the posix path of (original item of theItem as text)
end if
end tell
EOS`

        if [ $? -eq 0 ]; then
            if [ ! -z "$linksource" ]; then
                rm "$item_path"
                ln -s "${linksource}" "${item_path}"
                echo "\"${1}\" -&gt; \"${linksource}\""
            fi
        fi
    fi
    shift
done


To run


save the code above into a text file (e.g. alias2symlink)
execute chmod 755 alias2symlink
change to the folder where you want to convert the aliases in
execute /path/to/alias2symlink alias1 alias2 ...