I assume they dont have any resource that is THAT desperately needed and that you cant find elsewhere.
Plus even if not religious, I imagine many still rather keep them, be it to study them in hopes of figuring out how to fix them someday, or a 'what if' that just as they suddenly shut down, someday they will turn on again.
If so, then all of the Domain reforms and whoops, the idiots at the Persean Sector scuttled all their gates 'for reasons'.
Maybe if a nation had an interest in isolating itself from a theoretical Domain return, because their policies are not in line or something.
Barring all that, I would see them as monuments personally.
That's how I interpret the 'silent crossing thing, less of religious reverence (After all, the only shown religion says the Gates are literally the greatest sin. I am more shocked why the Pathers havent terrorist bombed them yet), but rather a moment of remembrance for the longe gone golden age of mankind.