Cannot stop script without sudo

[AlexEshoo]

I am having a problem stopping a script that I am running using the user option. I configured the permissions on some necessary directories to be able to start the service properly, but when I try to stop it, I get the following message:

kill: Operation not permitted

After some investigation I found that the PID stored for the init script is the one for the sudo -u <user> <cmd> command, and there is a separate one for the actual running script. I started the service and I cannot kill the process using kill <pid> using both the pid for the sudo -u command (stored in /var/run/<cmd>.pid) as the desired user. Any ideas?