No, I don't think you'd ever use Zealian. The noun is 'Zeal', and the - what's that part of speech? Whichever denotes the possession of something - is 'Zealot'. Therefore whenever one speaks of something belonging to or of Zeal, whether it is a person, a sword, or whatever, one uses 'Zealot'. The Zealots were a group, after all, and if one speaks of a member of their company, such as Judas Iscariot, you would say Judas the Zealot. If you speak of, say, a plot by them, you would say a 'Zealot plot' (for those that don't know, the Zealots were an anti-Roman group in Israel circa 0.)
Anyway, I truly think that the unification of the language into one standard is a simple gameplay quirk. After all, other languages DO plainly exist, such as Latin. Likewise does Greek for words such as Chrono. The only way to avoid this is to say that these are all transliterations from a base language that is spoken. This, then, would open the door to the game being an interpretation of truth (as all stories inherently are), and allow for multiple languages that are never precisely shown.
To be honest, not taking into account the shift in language is as grievous as not accounting for changing weaporny or clothing or architechtural styles in different time periods. I mean, would it be any fun if Zeal looked like 1000AD? The language is just another facet of the setting, and an often overlooked one.
Finally, just a note, Melchior itself is either coincidental, or a translation from the Zeal tongue into a later language, as Melchior is a real name - that it's a real name most people know. I'm not sure what it means, but Melchizedek means 'the king of righteousness', and in that the first part denotes 'king'. Therefore whatever Melchior means, it has something to do with 'king'. Likewise, Belthesar pertains to an ancient high god in some aspects, but more generally to the word 'lord', that is 'Bel' - this is given to many gods in the old world. So it is plain that one of a few things must be: the names are simply translations into later Akkadian etc. (my personal view), and that in Zeal they had different names; or that the real world can be fully discounted, which in light of crosses, cathedrals, AD, Latin, Greek, and such things as that, it cannot be; or, it is coincidence. I would tend to say the first, save with Melchior, which fits with a different meaning into my perception of the Zeal tongue. Just like Tolkien does with Samwise: his real name is Banazir, but it means 'half-wit', which in English rendering is Samwise. Even Lord of the Rings is given as an interpretation and retelling of the tales of the Red Book; I think Chrono Trigger is much of the same, and Chrono Cross is without doubt such (who has failed to note that it begins and ends with reading from a book, after all? Someone is retelling the story of Chrono Cross, it is absolutely certain. And everyone knows how tellings can get... changed.) Thus perhaps things in Chrono Trigger, and certianly not in Chrono Cross, can be taken at face value, and must be approached in the same way that any legend or myth that is re-told is approached: with cautions regarding how things would actually have happened, and how aspects change or are simplified in the telling. The Zeal language could well be one of those aspects performed by the storyteller.
On this last note, especially regarding Chrono Cross, what are the implications of this?