We are using the ESP32 as a replacement for Raspberry Pi quite a lot, in 24/7 applications. For your application, I don't think the ESP32 is wrong, it just needed to be used in an environment made for that application. That means, no "maker boards", but application specific developed boards, with industrial IOs.
When I understand you right, your boards are connected by Ethernet? If so, I would replace the batteries with PoE(power over Ethernet), when there is already a CAT5/6/7 cable installed anyway.
The on-chip watchdog (not only in the ESP32, but any MCU) can be disabled by a software error, a not so uncommon problem. Adding an external watchdog and reset supervisor is the common practice, to avoid these problems. Cost a few cent, but is bullet prove.
We have designed the EsPiFF, and ESP32 in Raspberry Pi 4 form factor. The upcoming version 3 will have an external RTC/Watchdog, plus 2kB FRAM, include Ethernet wired and Wifi.
https://github.com/MDCservice/EsPiFFI am currently designing the V3, for our Crowd Supply campaign. The EsPiFF does not have PoE, not enough space on the base board. But I could add the same headers for PoE as the Pi3/4, so that a PSU on a PoE-HAT could generate any voltage. If you are interested, let me know.