Btw, finally I found that config option. You can choose from three options:
1)Leave it like it is (actually I really don't thinks there is any reason to enabling IC2 machines since auto-machines are practically same except different ratio for overclock upgrades + GT ones have advantages like autoeject, ability to use covers and other GT upgrades, energy outputing, etc.)
2) B:allowVanillaIC2MachinesFromAutomaticOnes_false=false <--- In config/GregTech/DynamicConfig.cfg, change it to true if you want IC2 machines. This way, if you want IC2 version of machine, you can just make it from auto-machine by shapeless crafting. This was true by default on 1.5 version of GT or maybe only in FTB universal config... I'm not really sure... However, this is used typically if you have some other mod which is using IC2 machines in crafting and not using oredict.
3) B:automaticmachines_true=true <--- also In config/GregTech/DynamicConfig.cfg, by changing it to false you can disable GT versions of IC2 machines completly... I'm not really sure, why you should do that.