If you are using runit rather than demontools, you will need to edit the run files that geoipdns-conf generates. Particularly, daemontools includes "envuidgid" which runs the listed program as the given user ID and group ID. The runit alternative is "chpst" which takes a -u option for the user.
Replace the contents of your /etc/geoipdns-1.2.3.4/run file with:
#!/bin/sh exec 2>&1 exec chpst -u geoipdns -d 300000 /usr/local/bin/geoipdns
Similarly, the /etc/geoipdns-1.2.3.4/log/run file should look like this:
#!/bin/sh exec chpst -u svlog svlogd -tt ./main
And that should be all you need. In a future release, we will integrate runit support directly in geoipdns-conf.