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You guys do realize BuildCraft is open source right? If you don't like the changes simply undo them... Or, instead of whining about how it should be a config, do it yourself and send a pull request. You never know, it could be accepted.
Also, if you do something like Ore > Pulverizer > Powered Furnace > AE System, it cuts out the step of sending the dusts back out to be processed, effectively letting you keep dust in the system.