I'd link the Panzerese language guide, but I can't seem to find the link. From what I've seen in it, and heard from the songs/cutscenes, a good bit of it is minimally altered Latin (as well as Greek I believe, but I'm not as familiar with it). "Sona mi areru ec Sancitu" probably took a lot of liberties with pronunciation. I wouldn't expect Latin to be easily spoken by native Japanese speakers.
You could assume they're spoken with classical Latin pronunciation (which might be interesting, giving more of a sense of a dead ancient civilization), or go with the Japanese pronunciation as canon.