Searching for a כלל גדול בתורה

Talia Friedman asks:

I was wondering,

How could HaShem have killed off 24,000 people if that was the last generation to have semicha? I understand that he was punishing them for sinas chinam yet why was he punishing the future of as yisrael? (my Rabbi just gave a speech saying how after the 24,000 students were killed R'Akiva gave 1 more smicha and was in the process of giving 5 more people semicha when he was killed. Then the Romans killed the one to whom he gave semicha, and that is why we have no more semicha.)

The Romans killed/tortured 12 Jews from then, Hashem killed 24,000. If any one of the 24,000 had survived we might still have real smicha. How could HaShem have destroyed real semicha?

These are hard questions.  I would defer to the Jewish Philosophy department, but I'm not sure they have answers either.  Why did Hashem allow His home to be destroyed?  How could he allow the עשרה הרוגי מלכות, including Rabbi Akiva himself to be so brutally murdered?  The gemara says that the angels asked Hashem this very question (זו תורה וזו שכרה?).  And that is all before we get to the unanswerable questions of the last century.  Imagine what life would be like with the בית המקדש.  Think how much Torah is missing because of these inexplicable tragedies through the generations.  If everyone from איוב to contemporary scholars have fallen short of comprehending Hashem's ways when it comes to these issues, at some point you study all you can, and then admit the imperfection of humanity's ability to understand the 'דרך ד, and move on.

I did see an interesting theory from Rabbi Ari Enkin (see the comments) that the 24,000 students who were killed were Rabbi Akiva's students who were pressed into military service (the first hesder yeshiva) in the Bar Kochva rebellion, and that they died in battle.  Presumably, the reason of שלא נהגו  כבוד זה בזה, is some variation of the שנאת חנם that destroyed the 2nd בית המקדש, which they were trying to rebuild under the Melech Hamashiach who they thought was Bar Kochva.  This would imply that he could have been Mashiach, but the flaws in the nation that led to the destruction of the בית המקדש were not repaired.  So Jewish History teachers - is it plausible?