I had the same problem and finally found a solution which as far a I can see is both safe and simple. A disadvantage of this method is that you have to take care of security updates when they are published.
What we are gonna do is make our own special shell which we chown and SUID to the user which we want the task to perform. To remain safe this user should be just an ordinary user without extensive system rights and place the script somewhere others are not allowed. Now we let php execute a script which uses this special shell and all command within this script will be executed as the chosen user.
In practice:
sudo mkdir /usr/lib/specialshell
sudo chown user_who_may_run_command:root /usr/lib/specialshell
sudo chmod 700 /usr/lib/specialshell
sudo cp /bin/perl specialperl
sudo chown user_to_run_command:usergroup_to_run_command specialperl
sudo u+s specialperl
sudo mv specialperl /usr/lib/specialshell
Now we make a script named command.script containing:
#!/usr/lib/specialshell/specialperl
$ENV{"PATH"} = "/usr/bin";
system("/path/to/command");
and from php code we use:
exec("/path/to/command.script");
et voila, no code change, just the name of command in php.
edit: works only with perl as shell, so changed bash to perl and put the shell somewhere safe