I don't know about the second part of your question on how to reconfigure pins.
To answer your first question, I don't think any MCU can guarantee absolute real-time as they do not have a real-time Operating system controlling them. You can achieve soft real time (https://en.wikipedia.org/wiki/Real-time_computing) using these boards. I am guessing the ST Nucleo support already supports that by default. You can check to see if there are overruns and without any overruns, I would say the model is running close to soft real time.
There are other boards that can do hard real time and can be programmed using Simulink.