[franga2000]

There is no reason the web server needs to have access to the database file, the application that needs it should be running under a different user.

[archi42]

If that's an option then that's the right way to go. There is a reason some MTAs have been doing something like this for decades now (I'm thinking of qmail).

To be honest, I'm not sure if it's even possible to run the application/interpreter/cgi (e.g. php) as a child of the nginx process - though with Apache I'm still seeing that occasionally.