Leif,
Glad to hear your liking JFBConnect! Always like satisfied customers. Unfortunately though, right now we don't have an easy way to limit the Content plugin. It's something we'll be adding in a future release for some other reasons (in addition to mobile enablement).
However, we love happy customers... so, while this hasn't been tested much, if you're up for adding a a few lines of code, this should do what you're looking for. In the /plugins/content/jfbccontent.php file, at line 21, you'll see the function onContentPrepare. Right at the top of this function, you'll see the first two lines.. add the $template line and return statement afterward as below:
function onPrepareContent(& $article, & $params, $limitstart)
{
$app = JFactory::getApplication();
$template = $app->getTemplate(); <---- ADD THIS
if ($template == 'rhuk_milkyway') <---- ADD THIS
return; <---- ADD THIS
....
In the if statement, make sure you update the check with the name of your mobile template, and you should be good to go.
Let us know how this works out, and of course, test. Good luck!