Yeah, you blew away the GD graphics library and the GDBM database library. Looks like your desktop needs them. :-) Boot it to runlevel 3 instead of 5 and use it in text mode. From there you can use rpm to assess the damage. Probably just forcing a re-install of the "gd" and "gdbm" packages would fix things. I'm not sure why your app's docs said to remove the GD libraries, that doesn't sound like a good idea to me.
BTW: you can find out if files are owned by any installed package by using a pipe such as this one:
/bin/ls /usr/lib/libgd* | xargs -n 1 rpm -qf | sort -u
If there's any output, then you know that you shouldn't remove those files because something else depends on them. I know, that won't prevent accidents like yours, but maybe it will help you down the road.