Have your program write the new interfaces file into a location to which only trusted users have access. Then write a small script which swaps the new file into /etc/network/ and restarts networking (via /etc/init.d/networking) and either run that script via cron regularly or have the user run it via sudo. You can also do some syntax checking in the script to make sure you're not creating an invalid configuration which leaves the network interfaces down.

Also, you didn't say why you want to do this, and most usage scenarios I can think of are better handled via DHCP, so maybe check that out first.