You could use winrm with any server local tool that works for you. You could find more information on winrm here or here. You could use appcmd as your server side tool, Information on appcmd is available on TechNet and on this site. If you still cannot get functionality that you need, write script agains AppHost APIs and execute it remotely through winrm. IIS7 doesn't have XML kind of APIs, and we don't recommend direct modifications unless you know exactly what are you doing. Configuration is much more than XML configuration files.
You also could install CTP2 of Powershell, CTP2 of IIS7 Powershell provider and use Powershell remotely. It is probably the most advanced way of dealing with IIS7 administration remotely.
I already fixed issue with bindings, thanks for pointing to it.
--Sergei