I agree that the biogenerator is a little on the weak side. However, consider this:
SirSengir balanced the ouput of the biogenerator on the differences of scaling between Buildcraft and IC2. You can read his reasoning in the Forestry thread on Minecraftforums. Most other IC/BC conversion mods base their conversion rates on the MJ output of coal in a stirling engine compared to the EU output of coal in a generator, which completely ignores this scaling. Buildcraft starts off generating less MJ than IC2 generates EU, but then ramps up sharply - lately made even more dramatic by Railcraft's steam boilers which are 10 to 20 times as efficient with solid fuels as regular Buildcraft engines. So, once you hit endgame, MJ is worth less than EU in terms of fuel cost, yet regular conversion mods keep giving you multiple EU out of single MJs. Therefore it's always a better idea to generate MJ and transform it into EU than it is to generate EU directly. The biogenerator, balanced as it is, intentionally stays clear of this issue.
(As an aside, liquid fuel boilers are actually pretty much in parity with Buildcraft, it's just the solid fuel ones that have broken scaling. That's because Buildcraft uses solid fuels for earlygame things and liquid fuels for endgame things, while Railcraft uses both in an endgame context, thereby vastly overvaluing solid fuels compared to the rest of the Buildcraft ecosystem.)
Also note that you're comparing the biogenerator to the magma crucible, which is (even after the nerf) still completely overpowered in terms of efficiency for effort, especially when run off solid fuel boilers. In fact, you could nerf it much, much harder and it would still remain an excellent choice.
I've described testing this in another thread, here's the summary.
Imagine that you just set up the infrastructure to produce a steady stream of biomass/biofuel. You now have multiple choices:
1.) Just plop down a biogenerator. Quick, easy, zero maintenance, cheap, just works. 200,000 MJ -> 32,000 EU.
2.) Set up magma crucibles, powered by either biogas engines on biomass, or combustion engines on biofuel, or a liquid fuel boiler on biofuel. All three are equivalent options, since converting biomass to biofuel is a zero sum game (you don't gain or lose any MJ in the process) and liquid fuel boilers orient themselves on the efficiency of combustion engines. Also set up an igneous extruder and have it generate cobblestone, which you then melt down for lava and feed to geothermal generators. This costs a lot more resources and effort to set up initially than the biogenerator, but it is also completely maintenance-free and gives you a great conversion ratio of 20,000 MJ -> 20,000 EU. Considering the scaling differences between normal IC and BC, this technically is already too efficient, but we're living in a world of GregTech and GraviSuit so I'm sure all those EUs will find a use somewhere.
3.) Use the same magma crucible -> geothermal setup, but use netherrack instead. This gives you a better conversion ratio, depending on the exact value the netherrack melting recipe is set to. However, it also introduces a maintenance overhead, because you now need a constant supply of netherrack which is difficult to automate.
4.) Use a liquid fuel boiler + steam turbine instead of the boiler + magma crucibles. The steam turbine is very expensive (although it becomes slightly cheaper in newer Railcraft versions) and requires you to occasionally replace the rotor, which is also very expensive. However, the setup converts 32 MJ/t -> 50 EU/t for you. That is a really excellent conversion ratio, and if you go through the trouble of maintaining a steam turbine, I'd say that's only fair.
However, isn't netherrack giving an even better conversion ratio for less maintenance cost? Yes it does, because the magma crucible is still overpowered. So what would you need to set the netherrack recipe to, in order to place it comfortably in between the infinite cobblestone setup and the expensive steam turbine? My testing has shown: about 16,000 MJ is fair. That's four times what it originally was, and still twice as much as it currently is. Keep that in mind when you try and make balance comparisons off of the magma crucible.
All in all, in the above list of options, the biogenerator is proooobably underpowered still. I'd maybe place it at 200,000 MJ -> 100,000 EU if I had the option in the config files. Unfortunately I don't, so I guess it stays where it is.