Love your work, but I doubt that this will happen. Even ignoring non-believers(of which I am one, before anyone gets twitchy with the reply), no matter how it's spun, it's going to piss off some group.
Not saying it's a reason to not do it. It's just an inherently religious theme, and you'll always get blowback.

Disclaimer: I am just passing on observations. I have no axe to grind with making this game.

I think the problem is likely the exact opposite. A lot of people do believe in this theme, many viewing it as a cornerstone of their worldview. For some of those, no matter how respectful Ben is, it won't be enough. For others, it will be too serious. For some, it will resonate. For others, it will be actively repellent. Same as any other theme, really, but I think the religious aspect will amplify those feelings a bit more than usual. So, I think that Ben should go in expecting flack. It's just the nature of the beast.

I'm not usually one for destroying a perfectly good game for a retheme, but I think you just hit my trigger point(and gag reflex). I'd have to turn it into a Chumbawumba theme on general principle! ;P

Ok, I should have noted that I DO have an axe to grind RE a Toby Kieth pinball

So, is the focal point the Red Sea split? I could see "Tower of Babel" being a Medieval Madness style centerpiece.

Of that I have no doubt. I was subjected to his music a lot in the midwest. I would happily sand his visage off of a playfield and replace it with just about anything else. Maybe Flock of Seagulls. Swap the music for the sound of two pieces of styrofoam being rubbed together.

To replicate the parting like this, you might ditch the single vice jaws and opt for multiple smaller jaws that open independently, allowing you to make it look like it is opening from one side first. Stagger the opening of each one by .5 seconds, then close them all at the same time.

The problem is not what people don't believe in, but rather what they do believe in. But I've already talked about that above.

If you are ignoring NT, I think that the part of the Red Sea is the top playfield action. I would also add a "destructible" Tower of Babel, ala Medieval Madness, because it would be flashy and easily recognized.
Might steer clear of the baby killing bits of the Moses story, which would throw out the plagues(unless you just ignore the last one). I'm fairly certain that bit would be overly controversial. You could do some desert wandering bits, kinda like the raft advance of White Water. Could be some good humor to be had from a Eden sequence. Have a mode where you throw apples at the snake, for example. A rain warning hurry up for a Noah's Ark sequence could be hilarious if done right.