Humankinds original refusal to accept the machines status as sentient beings led to the destruction of the earth and the creation of the matrix. I believe the current situation is actually evidence of the machines desire/intent to create a world where both speicies can live together, destruction of mankind does not seem to be a Machine aim, nor do I think it is attempting any kind of punishment here. Rather it seems machines have attempted to create a mutually beneficial environment yet relying on 'relatively' pure logic they are unwittingly acting in the manner of a police state and denying the full breath of freedom humans really need. Unwitting subjugation is perhaps what we see here.
Are the machines ultimately any better or trustworthy than humans is an interesting question that therefore arises - There are paralells between the humans treatment/ disregard for machines and the Machines own treatment/disregard for the Exiles.
It all smacks of a form of evolution as I have bored people with before, Humans develop through the relatively slow evolutionary process until they can create a superior/alternate form of life - in this case the machines, they in turn become aware and self motivating and driven by survival become termed exiles (this is the general term and not an argument for specific exiles such as the Merov). As each group is bypassed a lack of understanding/fear by their antecedents results in violent resistance etc. It may even be that the different exile groups are individual attempts at machine evolution to advance and survive (the merov may not himself be the most worthy but for the moment seems to have control etc)
Think of it like, when you are dreaming sometimes, you think the dream is real, and you don't know you are sleeping, even though you know somewhere in your mind you went to bed! ^_^