Now what I am wondering if I can do In-System Programming by powering up the mainboard and only use the data pins of the spi header. Problem is I don't know if this is possible, because CS# and DO are also on high level! And what do I do with the clk signal? Is it povided by the mainboard and messes up with the signal of the programmer? Or is it possible that the chip is electrically damaged, although I can read out its ID? Soldering it out is what I want to do last!
Check whether CS#, DO are connected by pull-ups with an ohmmeter when the system is shut down. I think I saw a board where CS# was wired that way. That way you can actively drive down CS# and be fine. However, I'd at least check whether there's bus activity before doing anything...