This is quite easy really. Talk to Ashur and agree to help him. Then talk to Sandra and walk out without kidnapping the baby. Go outside and watch the raiders mow down the slave rush. You can help out if you want bad karma. Go back out to the Mill. You can just hang back and let all of the raiders inside the back areas rush out to meet the slave attack. It's a fairly cool fight to watch from the upper level.
After that, just calmly walk to Midea's quarters. You can either pass a speech check or grab one of the notes on her desk to find out the location of Wernher's hideout. Go to the steelyard and head straight back. Go past Wild Bill's body and past the Wildmen's shack. Kill the one slave on guard duty and go inside. In my case, Wernher was already hostile. If you go in without a weapon drawn, then you might have better luck. You can use the Black Widow perk or pass a speech check to convince him to leave. Otherwise, just defend yourself. He is leveled to your character, so he might be incredibly strong. Just use your new weapons to wear away at him and win. Loot his body and report back to Ashur at Haven. Things are back to normal and you can now use the ammo press. Sandra will buy teddy bears for Marie.
The Pitt will still be open and functioning in a similar fashion regardless of your choice. The slaves still go through their work routines if you free them. The only real change is the noticeable lack of raiders in the event of a rebellion.
You can still do the Mill Worker quest if you haven't found all 100 ingots. Everett is neutral and marked as essential, so he should still be around to collect the ingots.
Marie's caretaker will start up an unmarked quest for teddy bears. She'll buy them for 30 caps a piece with 10 experience points as a reward too.
Finally, the ammo press is all yours. The ammo press is inside the mill. You can find it just past the large cage that looks down into The Hole. You can also look for the two steel crushers that have a terminal near them. The operation is fairly simple. You can load unneeded bullets and scrap metal into the material bin. Each of these has a relative value, with some more “expensive” bullets. For example, it takes 15 5mm bullets to make a .308 sniper round and vice versa. Just load your ammo up and use the terminal to make the bullets you want.
The real value is that most people should have accumulated a whole lot of useless ammo from their wanderings. The ammo press can take all of those 5mm rounds your sniper doesn't use and turn them into .44 bullets for Lincoln's Repeater or .308 rounds for your favorite rifle. You can always return to The Pitt through fast traveling to the tunnel, activating the railroad car, and fast traveling to the Mill. Keep this in mind.
That's it for the main questline of The Pitt. Congratulations.