I think what you're saying is that 'it' doesn't make sense because we're talking about people. But an enemy can be a person or a group. If we're talking about the former, to use 'it' would not make sense. But if we we're talking about the latter, it might. Let's say two kingdoms—we'll call them Rhizaria and Alveolata—are warring. If someone in the court of the Rhizarian king mentioned the Kingdom of Alveolata, the King of Rhizaria might say of that kingdom, "It is an enemy."
Late response, but 'It' is perfectly acceptable for people in English when the gender of the person being referred to is uncertain, or you don't know for certain it's a person, or even if just talking about a person in a really abstract sense (or in the rare case that the person both identifies as neuter and doesn't insist on something like 'xer' as their pronoun). Yes, English (like most languages) lacks a gender-neutral personal third-person pronoun (multiple attempts have been made to introduce one, but none of them have really stuck well enough to make it into any well respected dictionary), and yes, this ticks off some people, but it does not mean that the use of a generic third-person pronoun is incorrect for referring to a person (impolite maybe in some cases, but not grammatically incorrect).