Of course this is hearsay at this time but it does fit to answer the question as to WHY when the captain jumped out of the boat the first time... we did not act
And he had expected us to act, and was surprised (and angry) when we did not.
Even if the SEALs were not yet in place, the Bainbridge's own security personnel could have riddled the pirates and the life boat with 7.62x51 fire from their M-14s and maybe M-240s. Even with their M2 .50 cals.
If not worried about hitting Captain Phillips, almost anyone qualified with the 7.62 weapons could do that.
Given that they did not do it, I'd say they had orders (or at least "strong suggestions" not to do so.