Shortly after I was extracted and commissioned in Zion, I was given the task of eliminating exiled programs (via missions), and it became apparent to me that I was terminating these beings not because they necessarily did anything wrong, but because they aren't human and don't comply with the machines. I found this inhumaine because I felt like I was doing the same thing the machines had done to us before the truce. I see humans and exiles as being in a similar situation if you will. We as humans choose to wake up from the Matrix because we for one reason or another, don't accept the illusion that imprisons our minds. In a similar way, the exiled programs don't accept the same system of control that ends their existence when it finds them obsolete. We are all refugees of a system that we choose to live beyond.
In addition, I feel that just maybe we and the machines might have something to learn from the exiles. Sati herself is proof that exiles still have purpose and a right to exist. In working for the Frenchman, I've seen and learned things about the workings of the Matrix of which Zion has no clue, and the machines aren't willing to tell their operatives. Also, in getting to know the Merovingian, I've come to the realization that he is one of the most misunderstood of the figures in the Matrix. The Frenchman knew that the One was part of a system of control, even as he didn't know until he came face to face with the Architect himself. The Merovingian wasn't against Zion, he was against the furthering of machine control. Furthermore, the Frenchman has control over the exiles, and to be at odds with someone with that task is reckless in my view. Love him or hate him, he is the glue that binds the will of the exiles and exile operatives. I believe that without his flag binding them all, Pandora's box would really be opened...
Some see him as evil, as a program that causes nothing but trouble in the Matrix. I see evil as merely a point of view. The Matrix is the only home for the Merovingan and the exiles. We do what we can to protect it, not to destabilize it. Remember that none of the people that lead us as operatives tell us the complete truth. However, I find that I can be allowed to think for myself and find the truth in freedom.
((Sorry for the long-winded speach, but this is the best answer I can give at this time.))