In most cases, I'm going to have to go with everyone elses views on this except I do have one question:
Can this program collide with itself?
You say it reads and writes from the disk. If it takes
longer than a minute can it get in a state of confusion?
Overwriting files, doing one thing because of a state the program can cause are just a couple problems that can result.
If you don't have to worry about any such problem, stick with the current solution. If you do, you probably still want to stick with cron and just put up some intelligent checks.