Cannot remount /system partition even when rooted (Sony xperia M2)
Use a kingroot remover and replace with SuperSU  

King Remover V9

USE FORCE REMOVAL INSTEAD OF START

Once you have root with SuperSU you should have more control ! ( Kingroot works with a temp root ) 

Init.d is just a simple folder to hold network security tweaks ! ... However People use it to implement Before-Boot operations that aren't always to do with network security !