It is possible, that if the Machines try to attack the Merovingian, he knows it in advance, and undermines it.
I am a trafficker of information. I know everything I can.
outright delete him: it seems the Machines cannot simply 'unplug' parts of the Matrix, for some reason. In the Animatrix: Beyond, the ghost house is not cleared automatically but instead erased 'manually' by authorities in-Matrix. But why are 'rogue programs' not killed by Agents?
What are Agents?
Inside the Matrix, they are everyone and they are no one. Anyone that we haven't
unplugged is potentially an Agent.
They run on the 'bluepills'.
The Merovingian can control 'the regulars' of the Matrix (bluepills).
Look there, at that woman, my god, just look at her. [...]
He sends her a program.
I wrote it myself, [...] each line of the program, [...] creating a[n ...] effect.
He explains it.
She can't understand? [...] Soon, it doesn't matter. [...]
This is the nature of the universe. [...]
Causality. There is no escape from it.
In the Animatrix: Detective story, it seems humans can have some resistance on becoming an Agent, by their free will. Mr. Ash resist turning into an Agent. In the Matrix, after picking him up at the Adams Street bridge, Neo is still a bluepill but once unbugged they trust that he will remain a human.
But the Merovingian achieves controlling, or rather, manipulating, the humans in a way that they do not resist anymore.
No bluepills: no Agents: no threat.