That's not a relative (adjective) clause; it's a that-clause—a noun clause (warning: grammar terms vary). It functions as a noun does in its various roles: subject, object, complement, appositive, etc.
This that is a conjunction, not a relative pronoun.
See Merriam-Webster at that conjunction
English and Language Usage's "resident" authority, linguist John Lawler explains:
There are two kinds of clauses in English that are introduced with
"that". One kind is a noun clause (called a "complement"), which may
appear (like a noun) as subject or direct object. These are tensed
(finite) sentences with a "that" in front of them:
That you were shocked is perhaps not surprising.
I told him that you were shocked.
Source: (in a discussion of "clauses beginning with
Your sentence (which I've simplified here for purposes of illustration) is in the passive voice:
That the structure was a church is indicated by its eastward orientation.
Let's put it in the active voice to better see what's happening:
Its eastward orientation indicates that the structure was a church.
That the structure was a church is your that-clause. In the active voice, it is the direct object of the verb indicate. Indicates what? That the structure was a church. As a direct object, it functions as a noun.
In the passive voice, the direct object is promoted to the subject position, replacing its eastward orientation. Now the that-clause is the grammatical subject, and again, it functions as a noun.