Cortisol often gets the reputation as the bad guy, but this really isn’t true. Cortisol serves a specific function and its over-activation can lead to not so great things, but that doesn’t mean cortisol is necessarily the root cause. For example, during acute exercise and stress, cortisol helps mobilize energy and acts as an anti-inflammatory agent (even reducing pain).
However, those same benefits are bad when they are done in excess and form stimuli constantly signaling its release. For example, while cortisol is a natural process as a part of the stress response, too little or too much can be a bad thing. Excessive cortisol has been linked to suppressed immune systems, increased bone breakdown, and other metabolic maladaptations. But again, the question of “is cortisol bad” should be contextual. So while its acute response is needed, it has been associated as a result of overtraining-like syndrome and has been linked as an effect of sub-optimal nutrition.
So like any complex system, we need to understand what might potentially be causing negative adaptations and what processes, such as nutrition, we can control to mitigate excessive stress. Making sure your protein intake matches up with the intensity and volume of your training is a good start.