Well, I don't get the point what breaks your plugin.

Do you use a ul/li inside the ul/li of the sidebar?

Maybe it would be enough to change #sidebar ul to #sidebar > ul
--------------------------------------------------------------------------------
Yes, the plugin imports a tree structure into #sidebar.

Well, it has a very complicated css rendering by js.

I only suggest, I do not insist.
--------------------------------------------------------------------------------
Can you try to change

@ #sidebar ul @ to @ #sidebar > ul @
and
@ #sidebar ul li@ to @ #sidebar > ul > li@

I think this should do the trick and we don't need to add another class to the css. :-)
--------------------------------------------------------------------------------
Do you mean in application.css?
If so, it will not, whereas there are <ul>'s situated in <form> and only after that in <div id="sidebar"> in some places.
--------------------------------------------------------------------------------