1) the fatal result of rats being tortured to deprive them of sleep seems to have been traced to oxidative stress in the gut (there was an article on this here not that long ago)
2) while I don't have an easy reference, a number of studies have found that even strenuous exercise before bed does not seem to impair sleep. As with everything sleep related there could easily be lots of individual variation but in general I don't think it usually causes trouble.
3) the author seems to consider free running sleep entirely posistive, however I think it is likely to cause circadian issues in a number of people who try it and may be quite dangerous. I think in my case going from a sleep deprived state to free running sleep (in an attempt to deal with insomnia) induced non-24 (it may be that non-24 has both a genetic susceptibility and a trigger event and that once triggered is essentially irreversible). In my case it also seems that there is an issue with internal coherence of the circadian rhythm with different parts of my body proceeding on different scheduled and rarely synchronized, leaving me disabled with memory issues and fatigue. So I encourage everyone to be careful when making changes to sleep schedules. For someone who already has a circadian issue it seems often better to sleep on the delayed or shifting schedule, but few people can do that without significant disruption caused by interacting with the rest of the world and there may still be some issues, at least for some people, due to being awake at night.
4) I think alarm clocks can in some cases keep a healthy circadian rhythm synchonized with the sun. Maybe consider them more like a prescription medication than smoking, try to avoid if possible but if using one can help you keep a healthy circadian rhythm then it seems likely to be healthier than a disrupted circadian rhythm. In my experience, when you wake up seems to be more important for setting the circadian rhythm than when you get to sleep.