Well Bullet Cluster or any other cluster is a problem for MOND. But the Bullet Cluster is also a problem for Dark Matter. The velocity of the Cluster is much faster than GR can provide, which MOND can easily handle.
I actually liken MOND to Keplers laws. It shows how the matter moves. If GR cannot reproduce it, then there is a need for a new theory. TeVeS is a patch which will not survive for very long.
The other problem is that GR and QM don't work well. Possibly when we a proper Quantum Gravity theory then we will find out how MOND comes about. MOND is just an indication of the problem.
I don't disbelieve in Dark Matter, but I am sort of convinced that there is something about MOND. It could be that both MOND and DM are correct. DM may exist in significant quantities in Clusters while MOND is sufficient at the Galactic levels.