An interesting, if unlikely, possibility...
"The Apology" is a thought exercise wrapped in the trappings of a story, yet if that sounds unappealing, read on. Determined to puzzle out how Kyon could've gotten over Haruhi's abuse of Asahina so quickly, Durandall has conceived of this tale, one in which Tsuruya plays an intimate part of the resolution. It is, in one sense, a logical extension of her fondness for being a tease, but it's hard not to recognize that Tsuruya, as written here, is being used as the author's plot solver. She does so in a characteristic, unique way, but her insights into Kyon and Haruhi's relationship are perhaps too accurate. As Kyon so aptly notes in the story, "[Tsuruya] is completely insane," and there's no other way to put it.
A story is often made or broken with how it ends, and what we have here is a Kyon who's gained no great insight nor received any revelation; his anger gives way to bewilderment and confusion, culminating in his usual resigned manner of accepting the world. In that, I think the story is weakened somewhat, though a great insight might be unworkable to fit into the canonical continuity.
All that said, "The Apology" is tastefully written, and Tsuruya's insights are nonetheless prescient and significant. The extent of Tsuruya's offer of friendship here (and all that entails) is worth reading, if only to experience the gamut of Kyon's emotions as he fully comprehends her meaning and intent.