Can I remove "be" from "had ordered to be shut the big river gates"?

This is a very hard sentence to phrase in a way that is both grammatical and easy to understand. The fundamental problem is that no agents are being identified. The best that I can come up with is

Someone thoughtful ordered the big gates to be shut where the river Ankh flowed from the twin city

Alternatively

Someone thoughtful ordered shutting the big gates where the river Ankh flowed from the twin city.

Of course, if what is meant is that someone complied with the order, neither of those fully captures the intended meaning.

At the order of someone thoughtful, the big gates where the river Ankh flowed from the twin city were shut.

EDIT: To clarify what I meant about identifying agents consider

X obeyed Y's thoughtful order to shut the big gates where the river Ankh flowed from the twin city

Even if you replace X or Y with "somone" we learn that there was obedience to a thoughtful order to shut the gates.

Yes- The second usage is correct. In the first sentence "to be shut" is the wrong usage because we have to specify first what we "ordered to be shut", in this case, its the river gates. So you could write Someone more thoughtful than the rest had ordered the river gates to be shut. I Think this is the correct usage in that sentence.