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The position of the LEver room has changed, now. That, or it just changes between seeds. Go past the Ballista guard, near to where the Caged stairwell is (the one you can't enter). Somewhere around there... there's a false wall to the left you can walk through, where the lever is hidden. Go along all the walls, I think you can see the lever room if you do

The balista guard is in the level 3 prisons right? I searched through entire prisons, there is no balista guard where I saw one in the playthrough. 

I may be wrong, but I'm not 100% the ballista guard always spawns. I think it's possible he's not there for you. I think...

The lever has been at the top of the prisons, toward the right end of the level, within another (unlocked, iirc??) room... at least for me so far.

It was suuuuper easy for me to walk right past the door to the interior room it's in, several times, because the doorway is kind of hidden.

Sorry, didn't realize the ballista didn't always spawn. In that case, you just need to start touching all the right and left walls in the place, until you see signs of a secret room, or go through one of them.