Lord Seeker Lambert was already dead before the events in the game. Cole killed him shortly after he broke with the Chantry specifically in order to try and avert the bloodshed that Lambert was planning. Lambert would never have agreed to the Conclave. Lord Seeker Lucius was the one in charge at the time of the Conclave and the one whom the demon was impersonating.
The mages originally dug in at Andoral's Reach. Even there they thought they had a good chance of holding off the Templars. It was a prolonged siege that would have been worse for them as they were so far out from civilisation with no supply lines. If they thought Tevinter and good bet, they would have found it far easier to travel north from that location and reach the "safety" of the Tevinter before the Templars could catch up with them. The mage rebellion was invited to occupy Redcliffe Castle by the monarch of Ferelden on behalf of all their people. Once there they could have concentrated on building up their supplies for a siege in case the Conclave did not work out favourably for them. With the degree of magical fire power at their disposal, sufficient supplies and the backing of the monarch, they could have easily held off the Templars. In Anora's case she even made an impassioned speech to win the people, in particular the nobles, over to the cause. Fiona's decision to indenture the rebel mages to a foreign power effectively betrayed the trust of the people of Ferelden. If Anora is in power the codex says it severely damages her standing with them. It was hardly a recommendation for what mages would do if given their freedom from the Circles.
The only thing I will say in defence of Fiona is that she did put it to the vote, not knowing that already the Venatori had infiltrated their ranks and so swayed the outcome in Alexius' favour. Whether the Venatori also used blood magic to influence the minds of the mages is open to question. However, you do see a Venatori working to influence Connor when you get to Redcliffe, so it is easy to see how they achieved their aims even without blood magic. However, if you do Hushed Whispers, Fiona is still in Redcliffe Castle in full possession of her faculties a year later. If they were going to use blood magic on her to control her mind, why didn't they do so? Same goes for that other mage who was against the rebellion and he hasn't even been used as red lyrium fertiliser.
I think it is telling the we meet various mages who have abandoned the rebel's cause because they did not like the way things were going. It was Rhys' vote that caused them to go through with the rebellion in the first place, yet he had left them prior to the Conclave. To my mind the Venatori spies had already infiltrated long before the Conclave and were helping to shape the thoughts of the rebel mages, including Fiona's perception that they were "losing" the war. If you want to call that brainwashing, go ahead, but a strong willed enough person, with the right convictions, would have resisted them.