Dale,

Admirals with "guts" don't blow people out of the water just because they can. That's morally wrong.

And stupid. There's any number of tactical and strategic reasons to board the vessel. The military did not know who precisely was aboard the yacht. There could have been unknown hostages or hostiles with valuable intelligence. The threat of capture is also a greater deterrent to would-be pirates than a speedy death, and news that pirates attacking US vessels are being captured and jailed will likely stave off some attacks.

There's also the fact that bodies of four US citizens were on board. The military maintains a deep respect for the dead, and will make every effort to retrieve intact remains.

The commanding officers weighed these considerations against the physical danger posed to their men by boarding operations, and concluded the risk was worth the reward. It's very likely that given the competency of US Naval forces trained precisely for this action that the actual threat was nearly non-existent.