Maybe this has been covered before, but I could not find it, so just wanted to share a quick fix for this. Personally I would love this as an option in the admin panel (to have 'Close on Reply' ticked or unticked by default). If there is an option for this, again, I could not find it, so I made a small amendment to the ticket-view-inc.php file, on line 498
change
<label><input type="checkbox" name="reply_ticket_status" id="reply_ticket_status" value="Closed"
to
<label><input type="checkbox" name="reply_ticket_status" id="reply_ticket_status" value="Closed" checked="checked"
basically just added checked="checked" to the code. not sure if thats the best way, but it worked for me :)
Anyway, just wanted to share that