Link: https://en.wikipedia.org/wiki/Mordechai_Vanunu

here is a poem he wrote while in prison in 1987: https://web.archive.org/web/20160708233137/www.vanunu.com/uscampaign/mvpoemspy.html

He developed a particular resentment for what he viewed as the dominance of Israeli society by Ashkenazi Jews or Jews of European origin, and discrimination against Sephardi and Mizrahi Jews from the Middle East and North Africa. He felt that he was looked down on by those who ran the Dimona facility due to his Moroccan origin. According to Dr. Ze'ev Tzahor of Ben-Gurion University, "he projected a deep sense of deprivation. He assumed an Ashkenazi dominance in Israel that encompassed all social strata and an Ashkenazi consensus closing off all possibilities of advancement for Oriental Jews."

So his real problem wasn't the Apartheid, but that Middle Eastern Jews like himself weren't profiting off the Apartheid in the same way as European Jews? This guy is peak israel.

So his real problem wasn’t the Apartheid

The text immediately preceding and following the bit you've quoted discusses his pre-whistleblowing activism which directly contradicts your conclusion.

You also left out this part:

Shortly before his scheduled release, Vanunu remained defiant under interrogation by Shin Bet. In recordings of the interview made public after his release, he is heard saying "I am neither a traitor nor a spy, I only wanted the world to know what was happening." He also said, "We don't need a Jewish state. There needs to be a Palestinian state. Jews can, and have lived anywhere, so a Jewish State is not necessary." "Vanunu is a difficult and complex person. He remains stubbornly, admirably uncompromisingly true to his principles, and is willing to pay the price," said Ha'aretz newspaper in 2008.

"This guy is peak israel"? really?

My interpretation of this, is that feelings originated because he was not benefitting from israel and was facing discrimination, similar to Palestinians.

He didn't even disclose israeli nukes because of his activism. But because someone convinced him he could get a million dollars for it. Unless Wikipedia wrote a biased article, there's not much ideological conviction based on selfless sympathy for Palestinians.

Compare this to a story like Rachel Corry or Aaron Bushnell and it's night and day.

The action was good but the reason looks more like self-enrichment than activism. Not much of a champion of the Palestinian cause. I prefer Gideon Levy.