I don't think it's a given that Thomas would end up a prisoner inside Demonreach, but I think it's a near certainty that Thomas would given sanctuary on the island itself -- even if Thomas had not been captured by the Svartelves.
Harry and Lara have access to exactly one place that they could stash someone, in perpetuity, and be assured that the Svartelves couldn't grab him.
Yeah, I don't think it was a given that Thomas would end up a prisoner under Demonreach either. If he was just staying on the island, Justine wouldn't need to be let into the island's defenses (at least no further than she'd already been). They can chat on the Whatssup Dock and avoid the worst of the island's creepy vibe. Lara probably has safehouses that the svartalves don't know about too.
The fact that the opportunity to get Justine past Demonreach's defenses wasn't too likely to occur points to an alternative main goal and the Demonreach ploy being a last minute change of plans hoping to get lucky since Justine's cover was going to be blown soon anyway. So what was the original goal of sending Thomas to assassinate Etri? I see two main consequences of initiating the assassination with Justine: (1) small temporary disruption of the Accords, but the peace talks were already going to be majorly disrupted anyway, and (2) it tied Harry's time up completely before Ethniu got there.
Consequence (2) seems most likely for Nemesis, and it synergizes with the distraction that the White Council vote. That begs the question, what was the thing that Harry was being distracted from?
Did Nemesis give up that agent? Unless Justine turns up somewhere no longer infected or dead, she is still out there. Oh they want the prison population alright, the frontal attack in Cold Days didn't work, they managed to get an agent inside, Maeve, Harry didn't have working knowledge of the island's defenses yet, but they failed. Oh I think it was predictable to a degree, that if Thomas survived the assassination attempt, Lara would want to free her brother, Harry would want to free his brother.. If Lara had her way, she would have hauled him off to the estate and fed him up even if it took a thousand vanilla humans dying in the process to do that. Harry also as a member at a critical time had only one alternative, put Thomas in prison on the island, that is the only solution that would satisfy everyone. Poor Justine, of course she'd want to see her lover, another in to the prison.
Now that Harry knows Justine has been taken, Justine can't do anything active to help Nemesis. At best, she's a hostage instead of a well placed spy that can act in Nemesis's interests. Nemesis gave those options up when it sent Thomas on the assassination.