I'm configuring a Fedora server to use a static ip (although this question should apply to any Linux server). Unfortunately, I don't have much control over which of the two ethernet ports gets used. I was wondering if there was any harm in configuring both ports to the same ip as long as I know only one port will be used.
No, there is no harm as long as you are sure that only one will be in use at a time.
Side note: You should really steer clear from Fedora on a server. It has a short support cycle and you have to upgrade OS versions once a year in order to get patches. CentOS is from the Red Hat family like Fedora, but has a much longer support cycle.