WordPress MU

I currently have a few, carefully selected plugins in the wp-content/plugins directory and I allow users to enable the plugins via the backend menu. But I want to disable the plugins menu now and move the plugins into the mu-plugins directory.

I've found that plugins must be placed directly in the mu-plugins directory and not in a sub-directory as they can be in the plugins directory.

Is there any way around this?

Many plugins will work fine if you only move the main plugin file I believe.

or you edit them and just change the paths, its no big deal, but it would break again when you update them.

I like keeping folders in my mu-plugins.
This works for me.
Example: create a folder in /mu-plugins/ called mu-widgets
Place this file along side the folder and all widgets in the mu-widgets folder will be included.
<?php
$mu_widgets = glob(dirname(__FILE__).'/mu_widgets/*.php');
if( is_array( $mu_widgets ) ) {
foreach ( $mu_widgets as $mu_widgets ) {
if( is_file( $mu_widgets ) )
include_once( $mu_widgets );
}
}
?>

We also rename all of the files in those folders to make our lives a bit easier. Plugins for blogs get named plugin_ Widgets get named widget_ etc.

Alternatively try using Plugin Commander which allows you to set plug-ins on a per-blog basis.