Naruto's Academy graduation demonstrates that there are other ways of graduating other than passing the final exam. Naruto graduated for his mastery of an A-Rank, forbidden technique, which is impossible for most ninja, let alone an Academy student; whereas the clone jutsu required during his exam was only an E-Rank technique.
The technique used for the exam is also selected by the teacher and could have been a technique other than the clone jutsu for Lee's class. For instance, the series has used matches between students for examinations. Or perhaps the instructors simply recognized Lee's talent and graduated him on his tai jutsu alone.
