I believe the only thing that is supposed to directly accesses /etc/hostname is the startup script /etc/init.d/hostname.sh.
Your apache configuration may depend on the hostname being a certain thing. When you setup apache did you use IP addresses in your configuration or the name that was in /etc/hostname.
If you have a mail server setup it could also be using the name from /etc/hostname. Though localhost.localdomain is what is in /etc/hostname, then I suspect your email system is partly broken already.
I believe it should be pretty safe to change the file. Change the file, run /etc/init.d/hostname.sh and then restart any services you are running like apache. If there are issues the fix should just be a minor edit of a couple configuration files.
If you are really paranoid you could copy the production system into a VM, make the change in the VM and then see what breaks. If you don't already have a test environment now might be a good time to set one up.