Wand of Allure working on pets for instant charm?
 

Is this working as intended being able to use a Wand of Allure on a pet to instantly poof it?

yes

What pet would be important enough to charm to poof it? Charm the master instead and it poofs just fine. Bards are perfect for this in PoHate for example with all the annoying Mage and enchanter pets.

he's on red

Then post in red forums not here please if this is some PvP issue.

Using wand of allure to instantly charm an NPC with a pet or an NPC's pet should despawn it. That is correct and working as intended.