Intermarriage in Israel is Taboo/going off the derech and staying married to a fully religous women is also a no-no
1) While those might be no-nos, I would hardly call that Anti-religious
2) Benda and Maria are not married, and Dubi only expresses his desire to stop being religious at the very end - he wears a kippa until the very last scene he is in.
3) Earlier you mentioned that you haven't seen it on Fauda/Shababnikim, but the same type of relationships exist - Shirin and Doron on Fauda, and (although I didn't fully watch it) Avinoam and Shira on Shababnikim.
4) If anything, Benda Echoes some remorse of being with Maria in their last scene (in the hospital in bogota).
5) Dubi is very complex, dealing with all of the PTSD from Azoulay's death and Yaeli's death/dissappearance/re-appearance. He's not some guy who just abandoned religion at random.