From a reliability stand point, I don't see an issue with the Raspberry Pi - I ran a Raspberry Pi (3b) based ADS-B receiver for a number of years with the Pi mounted in a sealed enclosure and the only problem I experienced was a damaged PoE splitter caused by water leaking into the ethernet cable. The splitter was not a part of the Pi and the Pi itself sustained no damage, I just lost the ability to communicate with it.
The Pi runs a debian linux based OS, so that aspect of the requirement is met, although I suspect you might need to recompile the app for it to run on an arb arm based processor.
You say you want to retire the lock controller and drive the locks directly from the SBC - I have the following questions ...
1 - how do you plan to drive the actual lock mechanism from the SBC? Most SBCs have limited current sink/source capabilities and will need some sort of an interface card.
2 - how do you plan on interfacing the FOB to the SBC? There are different types of FOBs and a reader of some sort is going to be required, which will also need to interface with the SBC.
I can see you replacing the mini computer you're using as a bridge now with an SBC but replacing the lock controller itself will present a few more challenges.