Q: remove facetime on El Capitan

The FaceTime app is part of OS X and cannot be removed.  You can however turn off FaceTime.  You can also go into FaceTime preferences and make sure enable this account is not checked.

Really QUIT Facetime from the menu, grab the Dock icon of Facetime and move it off the dock while holding, wait a second while holding then let go it disappears in a puffff.

Then open SystemPreferences->Notifications  select Facetime at the left, on the right uncheck all boxes and set Facetime alert style to "none". Then quit SystemPreferences.

To be sure Logout (from the apple menu), then login again.

That should do it.

Do you have family sharing set perhaps.

I do not have much experience with this.