Dips shouldn't kill it (unless it's inherently unstable) but spikes definitely can.
Spikes can be addressed with appropriate input protection. A big, low-value resistor with a TVS behind it should take care of spikes.
But this shouldn't be a difficult problem to solve. Converting 48V to ~5V is extremely common in PoE equipment. There are numerous off the shelf designs designed for it. It's likely you were looking in the wrong place (e.g. searching for "buck" instead of "flyback").
Most Wall AC Adapters will operate at 48V. This has been used by the ebike community for a while to power lights and accessories. I use an 120VAC molex hdd ac adapter to get 12V and 5VDC out of 48V batteries.
If not for being mechanical, I could imagine using a 48V motor and a 5V generator; both can be 95%-98% efficient.
(I think perhaps his irrigation pivot needs 3-phase power. I'm pretty sure all of his well pumps are run by de-tuned automotive engines converted to run on natural gas.)