My old military mind went to "assets" meaning either: 1. People you have within another group or organization (i.e. either someone you've embedded in a group, or someone already in the group that you've recruited to provide information to you). As in "we have an asset in the Frontier Development Group that reports to us through back channels" (don't we wish!!): 2. In some contexts the crew themselves may be considered "the assets" (e.g. "the biggest asset of the ship is its crew"). That might change the tone of "liquidating the assets". Were the crew liquidated by someone already on board the Cap ships rather than by the attacking ships? And the term "liquidated" generally also carries a different connotation than "killed in action". Trying to look at the wording from some different angles.
I think of "assets" in this sense as in:
1. Valuable.... not the crew. A crew is expendable. In this sense as I think we need to look at this as the ships and crew are a way and means to an end...
2. The assets are either data (Palin's) or high-value target individuals (human) or alien life forms....; or
3. Alien tech, a ship, etc.
The crew of these ships exist only to deliver their cargo. If there is trouble at a certain critical level, elimination of the crew could be protocol to protect the secret. I think that the assets are likely either the stolen data or as likely, alien life or tech. To protect the secret, even the object is to be destroyed. Age old human trait... "If I can't have it, you won't either.".
Whoever send the message was an "asset" of the shadow entity behind this entire escapade. But that entity asset was watching over something far more valuable. "Suicide" mission if it comes to it. Destroy the cargo/assets and possibly yourself, if necessary. This was no cleanup. If it were, everything would have been vaporized to leave no evidence of any kind. This discovery is a "mistake" or a "plant".