my opinion is that nicodemeus was more upset because he did not get any say about the existence of that organization, i mean he is a predator and if you remember how thomas justified fighting for th "right" side in "backup" the you shall realize that nicodemeus considered the black council as a potential threat by its very existence; so the burning of arctis tor was something  that nicodemeus did not know about and as the premier individual when  it comes to bringing about the apocalypse he certainly did not want to share the spotlight with anyone,especially not people so secretive as to elude him,ad so powerful as to storm the HQ of one the major superpowers in the supernatural community