Personally I haven't had the chance to work with this application, but restarting the application is common approach, for example to re-read the config file, or any other file that's being parsed. So, your concern is whether this is normal or not. Well, if this is the only chance to update the exceptionsitelist, I don't think you should worry, unless restart takes too much time. BTW, what kind of application is that, I mean, can you restart it just like "/etc/init.d/dansguardian restart" or it's more complicated ?
I spent some time at the dansguardian's site, have you looked at the source code or at the Extras page ? Is there something that would satisfy your needs ?
I understand that I'm not helping much with this post, just trying to point the thoughts in the right direction, hopefully
Given this flow, it just came on my mind how I apply new rules at /etc/sysctl.conf file - "sysctl -p", so you probably need something like this.