I have mapped .minecraft folder via junction link to C:/Games/Minecraft/game folder, thus all of .minecraft content is actually located not in the user %appdata% folder, but in C:/Games/Minecraft/game folder. Also, C:/Games/Minecraft is used for Minecraft installation and had this structure:
/game - i have a junction link from .minecraft folder to this folder
So, whenever launcher is updading, game folder disappears and appears again, but with no content in it. So game is fully cleaned up.
Except for this, everything is working fine.