Keeping in mind this isn't the "whats wrong with Star Trek VI" or the "was Spock justified" thread, personally I don't have much of an issue with forcing a mind meld under these circumstances and can't think of any other way of getting her to tell them the information without resorting to another form of torture (if you can please suggest it).
As the Uhura and McCoy, it did make them seem a little daft seeming the history of the Klingons and Federation:
At no point has there ever been a study of Klingon anatomy through giving those either captured or killed a medical scan?
I get that Meyer wanted real books on the Bridge for the translation scene but it just seemed daft that they didn't have it in digital form and have the computer display what the border guard was saying and allow them to quickly compose a response without going through a phrase book.
The fact that an experienced communications officer should know how to speak basic Klingon is another point entirely, one which I am glad they have addressed in the new films as if she is can distinguish between 3 dialects of Romulan we could safely assume she can also understand Klingon.
Back to the Enterprise, Starfleet orders do suggest the decommission of the ship (unless Uhura meant the command crew) where as Kirks final log suggests the ship would go on. I think it likely that he knew that there was to be another Enterprise and he was referring to her as an entity and spirit instead of one physical ship, in Generations he refers to Picard as Captain of 'the' Enterprise not 'an' Enterprise (which may or may not really mean anything)