It's not a very good program for max reps. But I think it's more designed just like all of the marine training programs are designed - to push your limits. Most of the people who come there don't know their physical and mental limits and don't know how to tap into their energy reserves.
These grueling drills will let you in on two things: discovering your limits and seeing whether you can take it or not. So it's not just about how many pull-ups you can do, it's about testing character and inner strength.
If you need to get the most 1-set number in pull-ups and you really HAVE TO train them once every day....I would do two submaximal sets(a rep or two shy of total exhaustion) with 5min rest in between. Otherwise just tough it out with their program because it's there to push your limits and it will.