Real root can not change any thing on /system original files!
Based on my comment and Yasser's subsequent comment , I can conclude that the issue was the immutable attribute set on the file build.prop. If other files and directories also can't be edited or deleted, then they may also be having the same attribute or append-only attribute. 

The remedy is to use this command with root privilege:

chattr -i FILE_PATH    # FILE_PATH is the file which currently has immutable attribute


Use -iR followed by a directory's path to remove immutable attribute from a directory recursively.

It is to be noted that OP already has busybox installed. chattr and lsattr aren't the utilities found natively in Android.

Relevant info about the used chattr command and append-only attribute can be found in my answer here.