While I flatly reject the reading (...)
That might be the root of the problem. Firstly, if two people - one of whom has no stakes in the matter - tell you, that your tone misfired and you are concerned about your tone, it might be prudent to take a step back and reconsider where and why things went wrong. Secondly, it reads to me as if you consider illegible's analysis as being out of the ordinary. It isn't. It's by far the most widely discussed theory about Gale and Mystra's relationship that I have come across. And while I disagree, it is still interesting to see why so many people come to that conclusion.
Moving on:
Now if I would make a Justice for Mystra thread I would ask why Elminster didn't show up at the party to tell us that Gale-bomb Gale is now enjoying his afterlife in the best library in existence.
Because he isn't. Withers catches Act 3 Bomb-Gale's soul before Mystra can whisk him away to Elysium and brings him elsewhere because Gale apparently still has stuff to do.
Whatever things were in EA, in the current state of the game the Karsite Weave connected to the Crown, the tadpoles and Gale's orb is different from Sharan Shadowmagic.
The Annals of Karsus describe the orb as a battery that gathers energy so the wearer of the Crown can use magic while being disconnected from the Weave. It is basically a parasite, which is probably also why Mystra calls it a "corrupted, half-born magic". She stops contact with Gale because the orb is dangerous for her, she however never seems to lose track of him as she states that she witnessed his whole journey.
Her reason for interfering when she does is because it is her chance to get rid of the Absolute, the Crown and the Orb in one swoop when Gale gets involved in the matter. You can learn during the Audience with Origin-Gale that it is not her place to destroy another god's creation, so she cannot destroy the Crown (or the Orb) herself. Gale, however, as the heir to Karsus's power, has no such limitations. This ups the stakes. In Gale's Origin, you are no longer only following your goddess's command on a path to redemption, while forgiveness and a place in Elysium are still the reward offered to Origin-Gale, the dilemma becomes one independent of obedience: How valuable is a single mortal life? Is it worth throwing your life away to rid the world of the danger of human ambition once and for all, or do you value your life and human experience more?
I do really enjoy the interactions with Mystra in Gale's Origin. It clearly shows the power imbalance between the two. Mystra feels more like a stern but kind teacher than a former lover, putting her in line with all the other maternal authority figures in Gale's life (Tara and Morena, his actual mom), but she also acts as a voice of conscience (as which the narration uses her for throughout the play-through) that questions your actions but which you can also challenge yourself. Basically, you can use the audience as a re-examination of Gale's faith, if you wish.
Gale's Origin, to me, places a lot of emphasis on reason and thinking events through. Blind obedience to the divine (detonating the Orb in Act 2) leads to utter chaos and destruction because Mystra is more concerned with the stability of the Weave than with the many, many lives she would ruin with her command. Detonating the Orb in Act 3 becomes a call-back to Withers's initial question about the worth of a single human life. And Mystra too becomes a more complex figure. It might be my interpretation, but I got the impression that while she had to ask self-sacrifice of Gale because it would be the best solution for the Weave, she as an entity much prefers it when he returns the Crown and distances himself from her. She seems to be self-aware enough to notice that being close to a god or being their Chosen is not good for a person. Her parting words when returning the Crown (and not requesting to become her Chosen again) are:
"Go, Gale of Waterdeep. Your life is your own at last. It's time you went and lived it."