Sorry for Necro.
Reading through Twilight of the Clans myself and took to the internet to see if there was ever an answer to who pinched Morgan. This specific thread was all that came up, maybe there is a newer one on this subject I've missed?
My gut tells me Morgan did it himself. All sorts of allusion and foreshadowing in Exodus Road and Grave Covenant of Morgan acting oddly from Andrew's perspective, and thinking fatalistically (from his own). Still reading Sword and Fire to see what comes of it and for a reason since he doesn't seem to be suicidal. One thought is that he saw it as the last catalyst needed to fire up the task force to take the fight to the clans. He also didn't have much respect from the various task force subcommanders, all who were debating orders like a "quilting club" as he put it. Perhaps he saw them more likely to completely obey/respect Ariana, the leader of the group most associated with the original star league, and that his death would benefit the campaign more than his continued leadership.
He also had not just a letter ready in case he should die, he had all of his operational orders, along with a personal message to Ariana, and an actual package for his family. I understand foreseeing the possibility of not making it and preparing your second in command, but to go out and purchase or find something emotionally meaningful to give to your wife and soulmate as a gift is something done more when you have some knowledge of your imminent death, rather than the standard battlefield risk every soldier faces.
Here are a few more of my thoughts as to why it was Morgan:
First off, the existence and presence of this Nekekami squad was known to only Theodore Kurita, Morgan, and the squads themselves. The ciphers and codes to activate them only known to Nekekami leadership, Morgan, and the squad.
The Nekekami acted on orders received far into the course of the journey. I doubt even HPG could have gotten such a coded pulse to the exact system where the spirit cat got his orders. Even if the speed was there to get it on time, delays like the stopover for water, the reverse jump after kicking the Ghost Bears around, and the drop off to maroon the Ghost Bears who would not become bondsmen; would have meant such a pulse had came and went by the time the ship reached that system. They could theoretically have continued sending the same message for weeks or months, but that would have represented a tremendous operational risk, so the orders had to come from within the fleet.
I have to reject outright that the Nekekami would double cross their employer. They view themselves as the foremost elite intrigue unit of the inner sphere, probably justifiably, and to even claim an association with them when there isn't one can likely get you killed. (See the books of the early days when Theodore hinted that he employed the Nekekami and they left a mask that could easily have killed him, needles laced with neuro-poison) They view themselves with the same sort of honor and pride that all the elite merc units of the IS do like the Eridani Light Horse, the Highlanders, the Dragoons, etc. Professional pride and courtesy dictate that you don't turn on your employer, even for a better offer.
If they were working for their employer when they murdered Morgan, than they could only be serving either Theodore or Morgan. Considering Theodore was making great strides in bringing his realm into cooperation, and that he was as focused on the clans as the greatest threat as Victor and Morgan, I can't see him doing this. It wouldn't serve him, even if he would stoop to the level of ordering hits, and as there are no shortage of competent generals in the Fedcom, any hit would have been done at higher echelons, victor would have been the most probable target.
If it had to be someone employing the nekekami, and it wasn't Theodore, than it had to be Morgan. I am just waiting/hoping for "the why" as I read further.
