UGH it's just SO IMPORTANT TO ME to make El have more than one romantic relationship (when it applies). Like, yeah, she was too young when Mike kissed her, and some people want to understandably do away with that part of her story, but that is INTERESTING. Lean into that! (Not in canon exactly—I would've liked for that to have been explored in the show itself, but it is more fitting for post-canon and canon-divergent fanfics)
Just because it is her first relationship and she's too young to fully comprehend it doesn't mean she isn't learning things from it. And learning what SHE likes and doesn't like in a relationship. Getting a frame of reference for future romantic developments, how people can treat you different when you're dating ("friends don't lie, but boyfriends lie all the time" + how Hopper cared about keeping her door open solely when Mike was over), what to expect when you break up with someone. Of course, they were not ideal lessons and she will probably see things differently as she grows up, BUT it is still a formative experience that her character goes through.
Not to mention her own shortcomings, too! She doesn't know yet how to communicate her feelings in a healthy way, she doesn't know how to look for support in a partner when she's suffering, and she hasn't yet considered how her actions (lying, as far as we've seen) can affect the people who love her. And all of that is good for storytelling! It creates conflict, it gives her character more depth—more importantly, depth that is not necessarily tied to her trauma as someone raised in a lab; it's just life stuff!
Canon has several opportunities for El to explore different relationships. After the S3 breakup, she could have explored things with Max. After S4, she could have spent more time with Lucas and feelings could have become muddy amongst their grief for Max. In S5, she could connect with Dustin since in S4 she went through some of the same things and felt the same anger Dustin was feeling at the beginning of the season. Any one of those would fit pretty well in canon-divergent fics, and maybe even all of them, since the moments don't really overlap. And contrasting all those romantic interactions against her time with Mike would create even more chances for character development for El and everyone involved.
I'm not saying you CAN'T develop El by erasing her relationship with Mike at that early stage—but there are already plenty of healthy developments to be had with that relationship existing. Therefore, you don't NEED to rebuild El from scratch in your fics; there's already plenty of interesting angles to explore by having her date Mike still young, but have it either end or change as she grows up and matures as an individual (yes this includes m11 fics but if I say/tag that, someone is gonna come bother me).
I guess my point is that you don't need to protect a character from everything "bad" or "problematic" or "traumatic" that happened to them in canon (or might happen in fics and AUs). Showing the recovery from those moments, showing that they haven't "ruined" the character is also interesting, important even. It shows hope, it gives your story humanity, gives it meaning.