I think a valid solution might be to detect at the end if any fuel value has been assigned, and only add one if there is none already.
As far as I can tell, this is already what the code is doing.
data.raw.fluid["crude-oil"].fuel_value = data.raw.fluid["crude-oil"].fuel_value or "100MJ"
What mods specifically should we be testing with?
I'm currently playing Space-Exploration with Krastorio and the "Gas Power Station" (which should be a Krastorio building) generates power recipies for all fuels with a fuel value. You might be aware that Space-Exploration lists Cargo Ships as a recommanded mod, so it took my friend and me a while to realize that we were kind abusing our power production.
I would actually totally fine if disabling the on-board generator would not touch the fuel value of crude oil. But I also think a proper fix would be to use a dummy sink to destroy an arbitrary amount of oil and produce an arbitrary amount of energy in return.