Again, I'm not really sure how much of this is still valid in D&D 5e, but the in AD&D Mystra had a bit more of a backstory and consists of three or even four deities. Faerûn's original god of magic during the age of Netheril was Mystryl. The Netherese had access to higher magical energies since the weave was still intact, sourcing so-called Weave Winds and casting spells up to 12th level. The Netherese abusive use of magic brought them the enmity of a species of floating, six-armed flatworms from the Underdark, called the Phaerimm, who were also extremely potent spellcasters and invoked life draining magic that slowly turned Netheril into a desert and caused trouble for their flying enclaves. Karsus was a prodigy, even by Netherese standards, and actually hoped to stabilise the Weave and defeat the Phaerimm, but of all the gods he could have used to fuel his spell "Karsus' Avatar", he chose Mystryl and, in a nutshell, short-circuited the magical Weave, killing the god of magic. It's difficult to tell if Mystryl had seen the end and didn't act to prevent it, or if the primordial god underestimated the power and ambition of the human Karsus. This happened ~1,800 years before the events of BG3.
The goddess Mystra was ushered into existence only moments later, but the Weave had already degraded to a degree that Netheril's floating enclaves were falling or at least crash-landing. Magic above 9th level was now barred from mortals except for Wish spells and True Dweomers that are essentially 10th-level-spells which can take month to prepare and are cast in elaborate rituals. This was the era of AD&D 1e, or the the first FR boxed set.
This second incarnation was killed during the events of the Avatar Crisis, also called the Godswar or simply the Time of Troubles, by the god Helm who was guarding the Celestial Stairway against the gods' avatars. The gods had been cast out of their divine realms by the over-power Ao after someone had nicked the Tablets of Fate. This is the same war that saw the deaths of Bane, Bhaal and Myrkul. While Cyric basically conquered the Dead Three's portfolios, Mystra had invested a portion of her power into the mortal wizardess Midnight who ascended to become the new Mystra after the crisis ended. While the new power was a little more good-aligned than the original neutral Mystra, the name Midnight faded over the following years and most Faerûnians clung to the familiar name Mystra. This was some 130 years before BG3.
I understand that this incarnation of Mystra was killed in the events of the Spellplague in later editions, and I don't know if there's an explanation how and why dead gods formed again after that.
Point being, the Mystra we meet in BG3 may have some inherited memories of Mystryl of whose energy the Orb was created, but probably has a different personality and makes different decisions. This also explained to me why she couldn't just reabsorb the Orb as it was the effect of an extremely powerful dweomer and consisted of energies which were not her own. Of course, I could understand why a goddess with such a troubled history of getting murdered would find it feasible to have nuke button.
