Guild Wars 2

I’ve done the quests leading to and way past Fort Trinity
I've even beaten the Sovereign Eye of Zaitan

The Fort Trinity Asura Gates work both ways.
However, the Vigil/Priory/Secrets-side fences are one-way. The gate-side guard lets you pass with a conversation. The other guard constantly says “access is forbidden”.

It is doubtful this is intentional; is there a fix for this?

I, too, have run into this issue. You can get to the Vigil, Priory, or Secrets headquarters via the Asura Gates at Fort Trinity, once you’ve advanced far enough in the story line; but once at an HQ, you are not allowed back to that particular Order’s Asura Gate to return to Fort Trinity. Interaction with the gate blocking access to the Asura Gate refers you to talk to the Gate Guard. The Gate Guard NPCs simply say that this area is under construction.

I figured that was just when I was trying to use Vigil or Whispers gates. I’ve had no problem gating in from the Priory, which is my faction on my 80, though I haven’t tested trying to turn right around and go back rather than coming to the Priory on my way to Fort Trinity from elsewhere.

Just adding my experience with this:
I can go from Fort Trinity to all HQ’s
My order is Priory, and I can get pass the gate keeper to use the portal the other way – regardless of when I try.
For Whisper and Vigil I can go from Fort Trinity to the HQ’s and back again, but only if I stay in the closed off area. If I come from the outside I can’t pass as “access is forbidden”.

This might be purely intentional, as I did choose Priory as my Order, so I shouldn’t get access to the other Orders services anyway – even as second command of the Pact. If I could, then it would only serve as a fast way to move around (Lions Arch/ Whisper/ Orr with no cost).
And the option to turn around is put in to aid people who took the wrong gate (it has happen) to get back without cost.