These MainMenu.nib's will disable Private Browsing mode and optionaly disable the history clearance.
They are tested with OSX 10.12, Safari 10.1
Will only be effective if your app is running in English
MainMenu1.nib has only the private mode disabled, MainMenu2.nib disables the use of private mode and clear history.
Select the option you want to use and rename it to MainMenu.nib
You can not simply put these modified files in the corresponding folder due to limited permissions.
First you restart your mac whilst pressing the following two key combination cmd + r
Your mac will start in system restore.
Just press in the menu bar 'utilities' and click on 'terminal'.
Here you will type 'csrutil disable' without quotes.
Press enter and restart your mac.
Now you can change the appropriate files, make sure safari is not running.
Open the application folder and right click on safari.
Choose "show package contents".
go to Contents/Resources/Base lproj
Rename the MainMenu.nib to eg MainMenuOriginal, like this you keep an original copy in case you want to clear history for example.
Copy one of the two supplied edited MainMenu.nib's into this folder. Make sure you removed the 1 or 2 in the filename of the edited files.
Open safari and you should see the effects.
Do not forget to redo the permissions. This time you type ‘csrutil enable’