What would or wouldn’t happen if Koresh was arrested while jogging?
Koresh was the sole driving force behind the group and the group appeared to need Koresh's daily presence to give direction and purpose. Even the advisory / enforcement council of 'Mighty Men' was totally subordinate to him as a council and as individuals.
My guess is that the arrest of Koresh would have been a huge blow to the group resulting and would have led to group members drifting off. Sure, one of the Mighty Men would have assumed leadership, but not to the same level of devotion that Koresh commanded. Some hard core would attend his trial and remain at the compound. But, once the spell of personal presence was broken, a released Koresh was going to have a hard time rebuilding the group.