Eeschema, least painful way of changing pin order per symbol instance
In KiCad version 5, cloning each symbol that you want to modify is the only way to go.  Otherwise, changing a library symbol will change all instances of that symbol on your schematic.
This is changed in KiCad version 6 (not released yet, currently nightly beta builds are available as v5.99).  You can modify each instance of your symbol independently.  You might want to try out KiCad version 6 to see if it works for your needs.