It's better to have the setup you want when you install ISPConfig - it configures various bits for you during the install. Something such as jailkit can't really be practically installed after ISPconfig without a reinstall.
Moving from apache -> nginx might easier to just remove ISPC, remove apache, install nginx, reinstall ISPC.
If you just want to disable some services, you can do that through the control panel:
System > Server Services > your.server
Untick the services you don't want anymore.
I don't think this removes the services, just disables them.