You can actually wipe out the Red Templars and rebuild the port without the Qunari.
Shame there is no active visible port there even after wiping out the dragon. Maybe it is because I am not working on the linear calander of story progression. Apology for the mistake. The operation wasn't a Ben-hesserth one. However the option via an advisior I think it was Cullen, was to use the Qun aid had you kept that alliance.
However the point made was how many ships containing Red Lyrium escaped in that time frame, without the Dreadnaught shooting them down.
Men die in war. Leadership is to calculate how many casualities there will be, through descisons made.
I do not consider for any moment there to be any actual gain from keeping a mercenary band alive whom are paid to die. The few to save the many. Outside of any prejudice or preference