The original sync_cohorts plugin that I was using was this one I don't know if that's what you have already looked at?
It's not perfect but it is pretty useful nonetheless, I have that script in my crontab along with the other ldap stuff (getting all of the users etc.)
Not sure what you mean by the cron not affecting new users? How often do you run it? I have mine running once an hour between 8am-5pm/Mon-Fri. Not sure if I should do it more, but as Moodle sites go I actually have relatively few students.
I have a seperate entry in the crontab for enrolments based off of our MIS system, so the sync_cohorts stuff you are looking at I only really need for 'default' courses that large chunks of people see (staff or students that sort of thing)
Let me know if that plugin/extension is of any use.
Derek