I have no dog in this hunt, but I just looked this up, and there's no indication he 'resigned in protest'. Their company news site says that he resigned after being sanctioned by the EU.[0] It appears heavily implied that he was forced to resign as a result of the sanctions – either directly (I'm not familiar with how EU sanctions work) or in that it made his position untenable.

[0] https://yandex.com/company/press_center/press_releases/2022/...

Edit: This report appears to bear out that the sanctions forced him to resign pretty-much-directly, as the company does business in Europe, and the sanctions prevent him from doing business in Europe: https://www.datacenterdynamics.com/en/news/yandex-deputy-ceo...