Czech Rep forcing citizens in AU to travel to Syd to renew passport

The Embassy have stated the facts to your friend, so like it or not that is the procedure. 

I suggest that your friend goes online and checks out cheap airfares with the different airlines. The red eye night flights are good so your friend can get there early, drop off the passport and then head back to Perth same day so losing very little time.
Wait 3 weeks then ring the Sydney office and if passport ready travel the same way get the passport and all is well.

I think you are over reacting when saying it would warrant a complaint to the EU Human Rights Commission.

Rules are rules and like it or not they are put in place for a reason.

When I was working in South Sudan I had to travel to Kenya, take my passport to Australian Embassy, then come back 2 weeks later to pick it up.

Thanks for taking the time to reply.

Just a couple of notes: firstly, Geraldton is 440km from Perth and flights to Perth are nearly as much at Perth/Sydney, so total return fares to Sydney can easily exceed $1,500, depending on day of week. Second, each trip will take at least three days (there are no red-eye flights from Syd-Perth, and only four flights Ger-Perth daily so you have no choice but to stay over an extra day in either Perth or Sydney each leg of the trip. So,with accommodation and flights combined you're looking at a minimum of $3,500 and six days out of your life--just to renew your passport!

Surely no on can argue this is a reasonable demand? And what of a family that might have 4 children in this situation?

Whilst I can see where you are coming from have you done any serious research ??
You can get a bus to Perth from Geraldton.
Virgin and Qantas have late night flights between 10pm and midnight Perth Sydney costing between $277 and $444.
Sydney to Perth Virgin or Qantas between 6 and 7pm costs $283 to $400

I travel frequently from Karratha to Gold Coast via Perth and Sydney  at a total cost of approx. $1600 for the 3 flights.