The stock messenger app can be removed, but its much easier just to set handcent as your default sms app.
Go to Settings>Application>Manage Applications> All
Select messaging and clear defaults. Go to gallery and share a pic by sms ( or just txt yourself) , a window will pop up asking if you want to use handcent or messaging, simply select handcent and tick the box to use as default. Now handcent is set as your defauly sms app.
Also go into the original messenger settings and turn of notifications to avoid getting dual notifications.