I just finished that quest today finally, and I feel the same way. The way the Archon was very Harbinger-like: taunting, grandstanding, etc. But, the Archon was an actual "person", so I thought a fight between my crew and him was imminent. Here's how I think it should've went down.
You sever the Archon's connection to the Remnant and he falls. You then rush over to your twin to see if he/she is ok. You try to rescue your twin only to find out that the Archon is still alive, blasting you away, and seriously harming your twin. He then states that it is too late and he is now more powerful than ever. He summons a couple of Ascended to fight you and your crew. Having had access to your connection with SAM and hacking into your neurolink, he tries to confuse you throughout the fight by randomly switching your profiles. No matter what you do, you can't seem to win. That's when SAM reverses the link and starts to shut down the Archon. After a long, gruesome battle, you and your crew stand victorious as you pull out your pistol to execute the Archon. That's when he reveals that he is one but many, and that the whole Kett race will declare war on the cluster. SAM reveals that he is able to extract some Kett fleet numbers/tactics from the Archon. You are given a choice to either hold him prisoner for SAM to extract any data or execute him on the spot, not trusting that having him anywhere near the Hyperion or Nexus would be a good idea. After making your choice, you rush to your twin's side yet again, only to see that he/she is nearly dead from helping to control the Remnant during your fight. You think all hope is lost, and SAM does the unthinkable. He states that although he regrets having to leave you, he feels his work is done and is confident that you will lead all of the races on the correct path. Despite your protests, he is willing to sacrifice himself to save your twin by repairing his/her brain.