Dissention in the ranks. What choice?

He offers you a clear run at the archon. Anyone loyal to him stays out of the fight.

Do you know of any dialogue differences of the mission is completed post-game? I doubt Primus would offer a kill code to her ship if she's superseded the original Archon.

I brought Vetra and Peebs with me to Meridian and got the opportunity to make a choice.

Well I didn't get a vid call with her if that's what you're asking. ._.

I genuinely don't remember because I thought it was supposed to be a post game quest

I told the Primus to kick rocks, because I was determined to find a way to take down the Archon on my own. I know better than to work with the enemy, even if they are my enemy's enemy. There is always a catch in those kind of situations.

So the option to take or refuse the kill code comes when you actually get to Meridian, not during the video call with Primus during this particular mission?

You can make a choice there though, you have an option to take a deal, or not, all while talking to Primus, I've just checked it. Check if you have a codex entry about meeting Primus after this quest. If you don't, then it got bugged, like mine. Apparently, if you bring Peebee, Vetra or Cora (don't know if one of them is enough for it to crash, or do you need two, I had Peebee and Cora with me) the conversation is over after the squadmate's comment about talking to Primus and you don't get to ask her anything or make any choice. The quest is completed, but there is no codex entry and nothing changes plot-wise. I have reloaded the game with Drack and Liam this time and after the comment I get an opportunity to ask Primus two questions and afterwards you make a choice.

So, there are TWO CHOICES to make in this storyline - one is whether to accept the deal with Primus or not and the second one (if you made the deal) whether to use the killcode or not (and save it for later probably?). I'm certain that this choice will be exported to the next game.

There is also a version of this quest in which it gets finished, but you can only hear a recording of some kind on the final console, you don't get to talk to Primus at all. I'm not sure how it's triggered though. Maybe killing/sparing the Cardinal has something to do with it? I don't know.

When I did this on my run I got to the console and primus started talking to me. But then as soon as a party member talked it was done. Like it just cut the quest off. Marked it as completed though so I was just like ok...And moved on. Didn't even know there was a kill code part of it..

Obligatory

It 100% got bugged, like mine, had the same issue with same companions with me. You either have to reload and do this part again, or you'll have to wait until your next playthrough.