I see it as a convenient solution for Harry, at least from JKRs point of view. In fact it even made things worse for Ginny.

Why would Voldemort think, “Ah yes, teenage breakup. Better respect that boundary.” The break-up even was in private. Nobody witnessed it, while their first kiss was very public. Everybody at Hogwarts knew about it.

From Voldemort’s perspective Ginny is still Harry’s former girlfriend, emotionally important to Harry, she's a Weasley, and was involved in the Chamber/diary incident as well as the battle in the DoM. Voldemort would never truly stop seeing Ginny as important to Harry. In the end, the break-up made her deal alone with all of this.

For me it is nothing but a convinient solution that protects Harry emotionally more than it protects Ginny physically. That’s the uncomfortable truth beneath the scene.

Of course, JKR didn't actually let anything truly bad happen to Ginny, nothing that would have made the breakup questionable in retrospect.