Steve was never the "safe" option for Nancy. Jonathan was.
Nancy has an ongoing trait of throwing herself into action to avoid feeling emotionally vulnerable, and hooking up with Jonathan after breaking up with Steve fits this pattern. She already shares a powerful emotional connection with Jonathan because of their shared trauma, which made him the perfect candidate to be her rebound. At this point, Nancy feels ambivalent towards Steve, a confusing mix of love and resentment. She's convinced herself that Jonathan is a better option for her because she's projected the traits of her ideal partner onto him, as seen in 4x1 when she's telling Fred why she loves him. And it’s easy for Nancy to project these traits onto Jonathan because she’s seen him display them – towards his family. He’s caring and compassionate towards his family. He’s protective over his family. He’ll never back down from what’s right for his family.
This is the biggest source of tension between Nancy and Jonathan in season 3. Nancy is expecting Jonathan to be all those things for her, to be compassionate and protective when she's being mistreated by their bosses at the Hawkins Post, to want to investigate the rat story with her because she's right. But Jonathan won't do that, because his priority will always be his family, and he doesn’t consider Nancy to be his family. This isn't a new trait either. In season 1, Jonathan doesn’t do anything to defend Nancy from Steve and his friends, only fighting Steve when he starts insulting Jonathan’s family. But the lady at the police station then convinces Nancy that Jonathan did this out of love for her, which contributes to her misunderstanding of him.
Murray is wrong in his assessment of Nancy as "retreating back to the safety of...Steve" in 2x6 (unsurprising considering he is, by his own admission, only guessing because she's "harder to read") but he's right about Jonathan. He has trust issues. This is why Nancy has to jump out Jonathan’s window in the morning rather than leave with him through the front door, even though Joyce and Will are clearly aware of her presence and their relationship. This is reminiscent of how Jonathan complains to Joyce about Bob spending the night in season 2. To Jonathan, Nancy has always been an outsider to his family unit, which is coming to a head now when he's choosing to stay with his family over his relationship with her. He also shows that he's projecting onto her too; despite telling Argyle about how ambitious Nancy is, he still expects that she'd give up her dreams to be with him in California and end up resenting him.
After their argument in season 3, Nancy says to Jonathan “I guess we just don’t understand each other anymore.” The truth is, they never did. They just happened to have intersecting goals in the past, which disguised their disconnect. It's not a coincidence that after making such a big deal about Nancy not being able to say that she loves Steve, the show never has Nancy and Jonathan say it to each other onscreen. If Nancy’s rat story hadn’t ended up being related to the Upside Down, this fight likely would have resulted in their breakup. Instead, Nancy gets to see all those traits she wants in a partner in Jonathan again (though still not directed at her. He does nothing to save her when she's about to get hit by Billy's car) and once again convince herself that he is that ideal partner, delaying their breakup.
Meanwhile, Steve has been growing into someone who actually embodies Nancy's ideal partner traits. This has always been at the heart of Steve's character arc. Nancy's character arc is about overcoming her fear of emotional vulnerability, which is the main reason for Stancy's breakup (she attempts to bury her resentment towards Steve and their relationship until it eventually explodes out of her when she was drunk, and she can't tell him she loves him). Her encounter with Vecna creates the perfect opportunity for her to finally address this flaw, to forgive herself and Steve for what happened to Barb, and to be honest about her feelings. Then she and Steve will finally be ready for each other.
The J*ncy breakup and Stancy reconciliation doesn't just make sense. It was inevitable.
