So far it seems warranted, this is the only case of a Pope bowing to an Islamic Queen that we have found so far.
How often do you think a Pope meets an Islamic Queen? There aren’t that many monarchies left anyway, and most of the Islamic Monarchies would not allow their Queen to meet a man unaccompanied.
This is about protocol - the media saying there is a breach of protocol. I have seen an image of Pope John Paul II bowing to Queen Elizabeth II of the United Kingdom. I’ve seen images of a Pope bowing to President Eisenhower - and Eisenhower bowing to him. I’ve seen photos of President George W. Bush bowing to a Pope. There’s nothing in protocol that says one Head of State may not bow to another - including Popes. I’ve also seen cases where Popes haven’t bowed - they’re not required to either.
Maybe you think the Pope should be rude to the Queen of Jordan. I think that would be silly. I would not want him to breach protocol by doing something excessive, but this isn’t excessive, nor unusual.