As far as I see, landing in Milwaukee was around 4:15PM, about 50 mins after STA in ORD. Given the departure delay in ZRH of over half an hour, that does not sound like they were holding a long time.

Sounds a bit strange to me, because the information about Obamas Departure from ORD was published and must have been known to the flight crew.
See here for example

I hope the captain got a big applause from all 233 passengers on board for excellence in flight planning.

Do you know if pax disembarked in Milwaukee or had to wait until they finally made it to ORD in the evening?