By installing a third party launcher you don't loose the function of apps like the Calendar and others. They are still installed as their own separate applications but Touchwiz does take advantage of integrating them into your daily use.
Basically if you install a third party launcher like Apex, Nova, ADW Launcher, Launcher Pro,GO Launcher, etc... you will still have function of the apps in question.. Actually when you install the 3rd party launcher they may integrate nicely or even provide their own versions of calendar, etc to work along with the launcher.
Touchwiz the "launcher" and "application list" portion itself will change by installing a 3rd party launcher but Touchwiz itself goes a bit deeper into the OS by means of the notification pull down toggles and other areas that a 3rd party launcher will not change so it will still be present in many respects.
Newer users to Android can be confused by launchers and UI's, etc.. Touchwiz/Moto Blur/Sense are all OEM UI's which are built onto the OS so they have more function than just the launcher, they also "theme" the device in their own ways aside from what vanilla android was built as.