The Merovingian tries to get in Neo's way twice: first by holding the Keymaker (which would prevent Neo from reaching the Source), and again by holding Neo prisoner in Mobil Avenue. Given that the entire Matrix system will crash if Neo does not return to the Source, it seems stupid of the Merovingian to try to stop Neo from reaching the Source. But it isn't stupidity on the part of the Merovingian, it is pride and lust for power.
The first way the Merovingian gets in Neo's way is when he holds the Keymaker prisoner. His primary reason for holding the Keymaker is probably to gain power of being able to instantly travel anywhere in the Matrix via backdoors. But, as discussed on the Merovingian: Oracle's Punishment page, another big reason he is holding the Keymaker is in hope that Neo will not reach the Source this time. He wants the Oracle's choice-based Matrix to fail, even if he is the one that causes the failure. In his mind, it still discredits the Oracle's choice-based model if someone or something is able to bring it down, intentionally or unintentionally.
If the Oracle's model failed and the entire human race ceased to exist, the Merovingian could probably still find ways to survive in Machine City because of the Trainman. Alternately, the Merovingian may falsely believe that a crashing choice-based Matrix would cause machines to revert back to the pre-Oracle Matrix that allowed the Merovingian to be the Prime Program, in order to continue researching ways to make a non-choice-based Matrix work. Either way, the Merovingian wouldn't be heartbroken if the Matrix were destroyed.
Later, Neo shows up in Mobil Avenue, and this tells the Merovingian that Neo did not return to the Source. This is quite an unexpected opportunity for the Merovingian - never before has any human (much less the One) fallen into the control of the Merovingian through Mobil Avenue. Next to the Oracle herself, Neo is the most important component that enables the functioning of the Matrix system. The Merovingian realizes that Neo is so important that the Oracle may possibly consider giving her "eyes" to the Merovingian in exchange for Neo.
So, this time, the Merovingian gets in Neo's way purely for his own gain of power rather than to prevent Neo from reaching the Source, because from the Merovingian's point of view, there is no way Neo can reach the Source at this point anyway.
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