I view it more as a cold war scenario, as well.
A shaper doesn't have the combat abilities to bust into Club Hel, kill 270 vampires, then somehow kill the Merovingian. Reverse the coin though - as a Lupine, or Elite Guard - would you really want to mess with someone who could re-shape you into a toaster oven?
But, let's take one step back even - these are all programs, and they have distinct "purposes". Shapers and archivists would definitely not want to wage a war, because it'd be nonsesical for them to do so. The Merovingian would find that conflict equally pointless, as he needs the Matrix in one piece, as it is his "kingdom".
I honestly wonder if the Merovingian is an exile at all. I mean - the exiles are not too different from the red-pills. Many exiles were programmatic parts of the Matrix, who "awakened" to the fact that they were programs. Yet, they can't be "unplugged" or go to Zion.
Since we know the One was created as just one more level of control to lead / fool / keep in line the red pills that got out, I've always viewed the Merovingian in the same light. Like someone the machines purposefully allowed to slip through the cracks, build up a empire - so that any program that did choose exile would not become a dangerous rogue (Like Seraph) - but would be swallowed up by the merv and thus returned to a controlled environment. (I believe a Crime underworld to be, in a funny way, a controlled environment).
Possible proof to this lies in a few places. We know that the Agents showed up every single time a red-pill enteredthe Matrix. It was only a matter of time. Since the Agents *know* where the Merv hangs out - you could just spawn dozens of them in Club Hel - almost no exile can defeat an agent. So, since the Merv is still around, you'd have to assume they didn't bother.
...and yet, they did bother with Seraph. We know the Seraph left the Merv once, and then we find out the agents bothered to track him down.
Interesting concepts.