Just like an impeachment proceeding, granting amnesty or pardon is largely a political move rather than a legal one. And it is usually done to serve the interests of the one granting amnesty. Remember how Gloria Macapagal-Arroyo granted Joseph Estrada pardon in order to ease up the pressure against her? The difference between a pardon and an amnesty is that the former is given to those who have already been convicted by a court while the latter is given any time during the judicial proceedings.
What gain would PNoy have by giving Trillanes, et. al. amnesty? For starters, it would be almost likely translate to an additional vote to support Liberal Part members in the Senate. Recall again that during the brewing battle for the Senate Presidency, the LP senators were a vote or two shy of getting their bet Sen Kiko Pangilinan elected to that post. Sen Trillanes could provide that vote all what’s needed to do was to get him out of jail.
The Senate Presidency has been long decided but it wouldn’t be such a bad thing for the LP to still gain Trillanes’ support once he steps in the Senate session hall.
Another possible gain of granting Trillanes amnesty is that once he gets out of jail and regains his parliamentary immunity as a Senator, he would then be able to continue his crusade against the sins of the Arroyo administration. He could do this in two ways; one would be through privilege speeches delivered on the Senate floor and second would be by testifying before 2010 Truth Commission.
Either way, Trillanes would be doing what PNoy could not have the balls to do; go after GMA and make her account for the wrong things she did while President.