One big hooray! My Macbook is back from repair and looks like it is working just fine :) I guess the people from the shop are happy, too. There were a lot of unpleasant calls and discussions :)
Well, in the pursue of being helpful and in case this information would actually help somebody... here are the places where they repair your Mac in Prague:
Clarexon, www.clarexon.cz, +420 266 711 687 - Update from 08/2012: Clarexon is now my first choice. Ask for Mr. Rangl for the best Apple service person in Prague :)
iOpravna, www.iopravna.cz, +420 226 211 650
Cesky Servis, www.ceskyservis.cz, +420 800 111 155
VSP DATA, www.vspdata.cz, +420 272 103 340
... I hope no one of you will ever need them :)