This guide assumes u know how to disassemble (how else did u gotten a rune in the 1st place).

To get a pet removal rune, u need to disassemble a rune, as result u'll get a lower level rune + a pet removal rune.
When u've a pet removal rune u double-click it. A drag menu will appear where u drag your pet in.
The menu will then show the pet-loaded runes and u select the rune u want to remove. The rune will be removed
(and will not return to your inventory).