What kind of stresses are put on the superstructure when it travels several times the speed of light? Shouldn't it peel the paint off a bit?
Oh yeah, the technobabble structural integrity field prevents the ship from essentially caving in on itself at warp. The Enterprise isn't fragile; I don't think a little water is going to hurt it.
Khan was working for Marcus all along, so it wasn't a question of "hoping" he would survive the attack- Marcus HAD to survive the attack. This also explains why Khan didn't just launch a missile from orbit: it would have taken out the whole building without being "selective."
Remember there is a huge conspiracy going on here conducted by Marcus. Kahn said he attacked Starfleet out of revenge, but Khan can't be trusted. It's very likely that Marcus (certainly more of a military strategist than young Kirk) would also understand that an emergency meeting would bring the heads of Starfleet to this "one room" vulnerable to assault (just as Kirk surmized)...
So Marcus instructs Khan to take out the best Captains of Starfleet in order to have a much more managable fleet under his control. It also explains the reason Marcus was so quick to promote Kirk back to Captain... So he could have Kirk be another of his pawns in his masterplan. Kirk is now full of fire and revenge over the death of Pike, and will do as he is told (keep the mission covert, take on a cargo of "classified" missiles) so long as the ends justify the means of Kirk gaining his revenge. However unbeknownst to Kirk, the Enterprise and its crew were all expendable on this mission.
That is, if you subscribe to a deeper conspiracy than what was shown on screen.
Kevin