In my view, even though I can certainly see the point regarding running and other forms of exercise, the problem is in the subconscious mind, which can never be fooled. The cilice, the discipline, the hair shirts are custom made to have a singular function: To repent before God and purify ourselves. They are part of the way we are led by God towards holiness. We can't say that using the cilice is a form of exercise, or that, even though we may get some form of physical exercise from using the discipline, that it is for exercise or physically healthful purposes.
Therefore, the mind knows that when one picks up the discipline, it is for a precise purpose that others for many hundreds of years have used it. Therefore, one is in harmony with a great tradition, and one is performing a clear action. Being in harmony with a great tradition is a powerful and supportive thing which brings blessings and magnifies our holy work.
Although you could of course say, "I am accepting the pain of this jogging as penitence", etc, in my view the challenge is that, at the same time that you are mortifying the flesh, you are also giving it health through that exercise, and the mind knows this, and you are also in harmony with other joggers, which of course it is great to jog and to exercise, but it is well known to be for different purposes, and something inside one knows this, and thereby the power of the renunciative act is diminished.