Assuming that you have exhausted all the other, safer means of achieving the same goal then in your place I might:

• Ensure AllowOverride is set to the smallest list feasible
• Create a user and group specifically for this task
• Ensure that only the files to be modified are owned by this user with tight perms (0644 should be easily lax enough)
• Set up suEXEC for just the one script to be run by this user/group
• Have an already-written contingency plan for when this system is broken into.