Bernard Marx changes a lot throughout the novel "Brave New World," and because of this, it is difficult to establish whether Bernard is really an enemy of the World State. However, the most likely answer is that he is.
The greatest threat to the system, according to this society, is an individual that is unorthodox. This means, an individual that is different from all others and who thinks in a way that is uncommon. This is certainly the case with Bernard, as he is able to feel jealousy, lovesickness and frustrated desire in a society that has "eliminated" it. No one else seems to share these feelings. Therefore, the accusations are true, as Bernard does exhibit an unorthodox behaviour.
The reason why the World State considers this kind of thinking to be dangerous is because it has the possibility of extending to others. If Bernard were to convince people to think like him, many of the assumptions of society would collapse, leading to chaos among people and to the end of the World State regime. I believe that, in some occasions, society is more important than an individual. For example, we create laws that restrict individual freedom in order to protect the interests of society. However, the World State takes this belief too far by completely ignoring the importance of a human life.