I'm glad you posted this! I like the concept that ships have to have a different sort of ethical code than their crews. (Your analogy to an abused horse is spot on, too.) The way Starfleet vacillates between missions and tries to have ships be everything to everyone has always bugged me. That Trager is confused and appalled by it, while Enterprise is just... resigned to it... is very true and very tragic.
Exactly what I thought after reading this too. Trek does lend itself to such stories as this one, when it comes to looking closer at these types of issues...
well thought out, and really a different style of writing in terms of the narrative!