Hi plugindoruk, remember that if you disable Domain Mapping, you also need to make sure sunrise is off.
Still, in theory -- if you are the only one that is going to manage site domain names -- you can indeed just change each sites domain name on a site-per-site basis in the network admin. In my experience, WordPress does not care about the domain name not being a sub(dom/dir) of the primary domain. I did a similar experiment in the days when Multisite was called MU.
The Domain Mapping plugin however handles things a little bit different and allows both Super Admin as site admins to control their domain names, add more than one and switch between them easily. This is not possible when doing it without domain mapping plugin.
There might be other effects too (plugins/themes) but I have not experimented long enough to run into any. And sure, Domain Mapping is not completely problem free in combo with other plugins like WordPress HTTPS either...