This is a problem in most Eastern areas. Christianity is, at best, a novelty to most Eastern developers. They use it in much the same way you see Buddhist and Hindu symbols used in America (as decoration, rather than out of understanding of the nature of those religions and what those symbols mean.) Shin Megami Tensei’s use of God and Christian symbols is equivalent to seeing a lucky Buddha statue in a Chinese buffet, it’s set dressing.
That said, the degree to which it is problematic is sort of up to you. I honestly don’t see the “God” in those games as even remotely representative of the true God. They’ve just kind of borrowed the name and the symbols. If it bothers you though, I wouldn’t play it. It certainly isn’t respectful, which is terrible, but then I’ve had enough experience with Eastern Games that I’ve kind of just come to expect it. They just don’t get Christianity.
If you’re a fan of the series, they’re actually releasing a new mobile game soon. I installed the beta like, just now. Looking forward to trying it out. Those games are definitely for hardcore RPG fans though, I can never get very far in them. Steep learning curve and punishing difficulty.
EDIT
In reviewing the game’s lore some more, I definitely see some issues with it. They really do try to paint God in a bad light… probably not the best series to be playing.