given the fact that we were actually unarmed during that scene - presumably the Lady-in-Waiting relieved us of our weapons when we entered the Sultana's chamber for 'security reasons', a big red flag that something was wrong (as there were plenty of times in the past where we met with Nanamo while still armed). They needed us unarmed in order for the conspiracy to work.
Hence once the deed was done the player's character could easily be arrested, meaning that they then spend the majority of time in that scene either laying on the floor powerless with their hands bound behind them, or faced with no choice but to flee. The Scions likewise are completely surrounded by Brass Blades and Crystal Braves - they're totally outnumbered (this probably also explains how Raubahn ends up losing against Ilberd, even with only one arm - Ilberd being the dirty coward he is probably had to zerg-rush him with his troops).
What struck me as odd was more how once the player reunites with Alphinaud and is introduced to Vice Marshal Tarupin, they're suddenly armed again. Where did my Curtana and Holy Shield come from? I like to think Tarupin recovered the player's weapon and returned it to them, but nothing is confirmed.