CESM does integrate w/AD, although it doesn't need to be installed to your AD system. If you install to your AD, you should have a more complete integration, rather than CESM scanning AD for updates to new systems and such. However, AFAIK, all control of the Endpoints occurs through the CESM Console. By assigning systems to Groups and defining Tasks for those Groups, you should be able to accomplish much of what you are wanting to do. Just as with a local install of CIS, you can define different network zones, and network rules for those zones; thus if you want systems to be visible/accessible to other systems when attached to the domain (versus DMZ, VLAN, etc) you can establish those rules - Globally or by Group. You should not *need* to disable the FW at any point.
However, the user will not be able to manually control CIS from their end. Depending on the type of users, this can be a good thing...

I don't think that CESM provides endpoint network access control such as you mention (scan before allow PC to continue to access network), but I could be wrong about that. You may able to define some CESM rules/Tasks that address that issue, especially in conjunction with AD.
Hope that helps, and hopefully I've addressed all your questions, at least to some degree. Please feel free to ask more, for more clarification.
LM