Of course we have some ideas about it, and of course there is a scientific method to generate those ideas. However, it's still a boat-load of assumptions, things that seem likely, and the best choices out of some very unstraightforward interpretations. Even the article you linked is full of those caveats. It's an educated guess, and while that's a lot better than having nothing to go on at all, it's still a guess.

I was taught both ancient Greek and Latin in school. While we were taught a certain pronunciation, it was immediately made clear that there were other pronunciations out there that were just as valid, and that other people who learned the same languages might pronounce things very differently. The pronunciation we used was seen as plausible at the very least, but we were warned that there was simply no way to be sure. As a result any plausible pronunciation was basically ruled as "correct".

If you go back to usage in a movie, there's certainly a method to use it in an internally consistent way. Pick one of the most-used pronunciations currently taught in schools, or just go with a modern Greek pronunciation (the alphabet is still largely the same) and make sure that everyone in the movie uses that pronunciation. But there's no way to be sure that that is historically correct in any way.