Personally, I don't think you'd fire from space to take out the top of the tower. That seems like a ridiculously difficult and narrow shot without a lot of purpose. Destroying the entire planet doesn't make a lot of sense either given it's Imperial controlled. I thought there was some dialogue about having to charge the laser longer to completely destroy a planet, so they might not have had the time. If the data was that sensitive, you'd have a way to just self destruct the station itself and it would be far faster to just hail the base commander to initiate self destruct than fly the Death Star there.
Whether intentional or not, a plausible explanation is that they didn't want to destroy all of the data housed in the vault. A DS shot into the ocean would create a tidal wave strong enough to wipe out all of the ground troops causing them problems, while the incoming ships could deal with the fleet. The shot narrowly hitting the tip of the tower could be just coincidental impact of the angle they used while firing into the water, but poetic justice for Krennic.