How do you gauge response from exercise? It's an important topic for athletes and one that doesn't come-up too often. Personally, I prefer to try and get feedback from athletes on a workout by workout basis regarding how they're feeling (healthy, ok, not healthy).
At first, I think many athletes are reluctant to provide this information for fear of how they may be viewed, but over time and when trust is built I've found athletes will be honest about how they are feeling, both physically and emotionally. Certainly, there are blood tests that can provide information on stress and inflammatory markers and this is important information. Lastly, a lot can be said for measuring resting heart rate and blood pressure values in helping to gauge response to exercise.
The training timer should not be automatically set to "go." One needs to gauge response to exercise as enthusiastically as promoting training sessions. Prudence here pays off in a big way when trying to head-off injuries.