Lairs & Citadels are currently too easy to Cheeze because they end the minute you kill the Maguffin. The Devs have made a very good suggestion for Lairs @ Improved Pandoran Lairs and Citadels.
My suggestion for Citadels is that you turn the Queen’s chair around, so that it is facing away from the Squad (preventing them from Sniping or lobbing grenades into anything in there), and start the Scylla in the conch shell, resting on her throne. She will not move out of her protective throne until Alerted – and she cannot be Alerted until a Squaddie gets round the conch shell and triggers her. That way, you have choose either to put at least 1 Squaddie in danger, to lure the Scylla out into Sniper range; or to mount a coordinated assault down one side of the map to get to her.
Either way, this prevents the current: Locate the Scylla – Snipe the Scylla – Win the scenario before the Scylla has even moved meta that the Citadel has currently degenerated into.