Didn't you notice that the coils on Brainpan's head were sparking as she was being shackled in the brig? The same coils that were previously shown to emit bolts of electricity whenever she felt intense emotions? Maybe, if Wildsong had tried to snap Brainpan out of her trance and get her sufficiently angry at Thunderblast leaving you two to die to save her skin, the resulting lightning storm could have shorted out your restraints and maybe cause two nearby guards to get electrocuted and drop their weapons.
I mentioned that Wildsong's thrusters wouldn't be disabled until the stasis cuffs were applied; and I was intentionally wording my posts to give you the opportunity to have Wildsong resist being shackled. With the guards so close to her, she might have been able to steal a weapon or two, short out her inhibitor claw, and try her luck at escape then.
In addition, if you had kept playing Wildsong when she and Brainpan were being led onto the train, I would have had two of the Ground Troopers mention that Brainpan's pet, Mutt, was still loose on the ship. Wildsong and Brainpan could have then devised a way to summon Mutt to them to help break them out.
After that, who knows? Maybe the two could have hid in the bowls of the Adjutant until the New Decepticon Fleet arrived on OL-2-C. Or maybe they could have made a break for a hangar to steal a ship and get the heck outta dodge. As I said: it wasn't impossible for Wildsong to escape. You had three opportunities to have Wildsong evade death- maybe more even; those are just the ones I can think of off the top of my head.
My policy as a GM has always been to give the players as much freedom as the structure of my games can allow- and I structure my games to provide the opportunity for characters to make a wide variety of meaningful actions that affect the game and the narrative. I'm not big on taking that freedom away at any point, and I wasn't doing that to you here.