Foucault on the church and state

In the lecture from March 15th in Security, Territory, Population, Foucault notes the way that the cosmo-theological continuum broke down in the 16th century so that political rule ceased to refer to ends outside itself (such as God) and developed a new immanent, secular raison d’État. Along with this the knowledge necessary to the ruler shifted from phronesis and knowledge of natural and divine laws to knowledge about the state, statistics. (Now let’s suppose, though Foucualt doesn’t talk about the present day church, that for the church this cosmo-theological continuum still exists and that most church members agree with it and agree to being governed towards transcendent and moral ends). The question is shouldn’t we be glad about this? Isn’t this, in fact, a fairly decent way to run church state-relations? And if so, does this make critique of the state a little more difficult? After all, what’s the point in critiquing the state for not being like the church? The state doesn’t recognise the same morality from within its point of view, from within its game, unless it is to see that it doesn’t undermine itself by losing the support of the populace. If one goes down this line, does it make less sense to focus on the church’s distinctive beliefs and practices and more on what common reforms and goods can be pursued with other groups?