Using Network Analysis in GIS and assigning constraints such as costs or speed limits or blockages to specified locations in the congested areas, one can find an optimum route to minimize congestion along the way.
Have a look at different papers on utility route choice models, which play a central role in stochastic assignment. Such as this one: https://trid.trb.org/view/481284 or Article Which road do I take? A learning-based model of route-choice...