You don't need to disable IrDA: the IrDA stack in linux needs to be connected to a low level IR device so it can talk IrDA. From memory, the IrDA transceiver on the empeg is on /dev/ttyS0 - which is what you should point gnokki at (or what you should do an "irattach" on to run IrDA).

/dev/ir is the consumer IR receiver, nothing to do with bidirectional IR.

Hugo