Hey Chris,
All you have to do is remove 1 line from the script to stop it from selecting-all...
keystroke "a" using {command down}
Modify the script.
Then add a Type a Keystroke action to the macro with ⌘↓ to get you to the end of the message body.
Or you change the AppleScript as JM suggests.
In general I prefer to have Keyboard Maestro type keystrokes, but it depends on the situation. Keyboard Maestro is less prone to side-effects from the user pressing keys on the keyboard.
-Chris