Well,
You could add json commands like {command:'removeMessage': 112} and things like that to remove messages. But that would mean you would have to keep a log of removed messages.. and edited messages.. in separate tables since if you just send the last x messages you wouldn't know if they were deleted or edited.
Or perhaps just an extra column in the message table status: active, deleted, edited (perhaps a date value)
And if the user wants to ignore someone, then you can indeed respond with a full reload or just use client side javascript to remove the entries by that user if you kept that information available.
<tr id="message_y" class="user_x">
Also, when someone isn't online and you try to PM them, it states "that user doesn't exist". Think it would be better if you would say "the user isn't online".
Anyway, you have seen the popup dialog screenshot, will you be fixing that?
I also attached a pic about the spacing issue, small issue but would be better if fixed

No space between date and "To/from" and after the name. Maybe if you used it would work better.
Also, a spelling error in the help: "usergroupds "
Edit: I would also love the ability to remove certain icons, like the button that empties the chat input field. And the ability to change the icon images.
Thanks