Ok everyone, thank you for all your help. I will share the information I got from Saudia and the embassy I called. So I called Saudia Arabian Airlines again, now not the Frankfurt office but their call centre in Riyadh. First spoke to a guy who didn't know what I was talking about and then got transfered to (I guess) his manager who spoke much better English. That guy confirmed I CAN fly via Riyadh with an Israeli stamp in my passport. As long as my stop over is not more than 8 hours I will not be refused boarding. Anything over 8 hours may cause trouble. Then, to double check, I called the Saudi embassy in Berlin and spoke to their consulate office. The guy there immediately said I do not have to worry whatsoever. It's only a stop-over and he also mentioned the 8 hour rule. He also added he has issued visas for people with an Israeli stamp many times, so even if I wanted to enter Saudia Arabia with an Israeli stamp, I would get the visa granted. This at least applies to the Berlin consulate, other consulate may be more strict.

Perhaps this information will be useful for anyone in a similar situation.