Been there done that! Yes, seem to be common problem with higher mileage Compass/Patriot vehicles.
Take your time, shop around. Not a critical fix! But the only fix is to indeed replace entire manifold.
I had to replace mine at about 140, 000mi. List price also was $318 for part. Thats list, you can do better than that. Unless the part has gone up in price, should be able to be under $400 to fix with labor.
As far as reprogramming, I don't know what reason there is to need to reprogram anything. Bottom line, get another quote.
FYI, in my case manifold runner was stuck open.
If your truly in it for the long haul, while the intake manifold is off and out of the way you might want to consider a cooland flush and change and new thermostat? But your only at 120k