@Marcin. Currently the plugin does not facilitate sorting of the folders. If you want to have that feature, then you have to edit the easyfolderlistingpro.php file. There are two instances in which JFolder::folders is called to get the folder list. What you need to do is to add your own sorting function to the class, and make that sorting function sort the list that you receive after calling JFolder::folders. I think the two functions that you will find the JFolder::folders call is customListFolderTree and formatListHandleSubfolders.
Hope this helps.
Feel free to share your solution with others once you get it working.