THAT won't pose an issue. Even vanilla furnaces can simply store "one value".
IC is already using that one value to supply whole cans of fuel... the number really doesn't care which value you assign to it. There won't be an issue with using one unit of BC-oil to provide X fuel points.
Adding the ability to pour multiple cans of fuel in would be possible... But I'm not sure whether it's within the range of what the Generator is intended to do.
How about we put this on the list for a special generator, which is meant to run off fuel, gas (if implemented) and BC oil, using said materials in a higher efficiency then the normal generator (if at all) with a higher EU output, probably about 30 EUt, too compensate for the incapability to burn simple stuff (wood, coal) as well as the fact you're using complex and limited fuel materials.
This I like that will finally make making fuel a viable option.