Eren in AOT and Akainu here are not at all in the same situation
So what ?
Eren is doing it for Paradis, Akainu is doing it to ensure that the sacrifices of Ohara Civilians weren't laid to waste.
Say Robin got on that ship, the buster call would have been just useless and all those civilians died for nothing.
Akainu's failure to kill every last Oharan scholar(robin) nearly led to Croc destroying the existing world with Pluton.
The thing is, Sakazuki did the right thing for the Marines. He says that a single scholar escaping would be enough to present a substantial threat to the World Government. The fact that Robin survived and what she did thereafter is a testament to that. Even before she joined the Straw Hats, Robin very nearly handed over the location of Pluton, one of the ancient weapons, to Crocodile, and now with the Straw Hats she is closer than ever to finding out the True History. If that's what the Marines wanted to prevent, Sakazuki did the correct thing.