I think if Gargantia was solely interested in de-escalating the situation and returning to the status quo ante, their best course of action would have been to ask/demand Ledo leave. The pirates come for their revenge and to reassert their dominance over the fleet and a limited engagement ensues. The pirates search the fleet for Chamber, don't find it, take some booty/slaves and leave, and everything goes back to the way it was before.
It's a less rational course of action to accept Ledo's "deal" if Gargantia does not wish to use Chamber's potential to severely cripple the pirates because it simply ensures that the pirates will continually attack Gargantia, both in an attempt to reassert their dominance (after being personally embarassed Lukkage
must attack Gargantia again) and in an attempt to capture Chamber. As Bellows said, Gargantia's weapons are meant to deter the pirates from attacking because the costs of conflict outweigh the spoils the pirates might obtain. However, with an "unused" superweapon aboard Gargantia, the potential benefit to the pirates in attacking skyrockets, so in the future Gargantia is probably more likely to be attacked by the pirates with Chamber on-board.
However, perhaps something in their culture obligates them to accept Ledo's proposal. The phrase "give water to the one who catches the fish" is used several times throughout the episode. Bellows mentions it to Ledo, and explains it is as a concept of "mutual aid", but it also seems like it is also an obligation to assist/protect one who has done something beneficial for you. Ledo then uses this phrase to secure acceptance of his proposed deal. When Ridget suggests to the Fleet Commander that they accept Ledo's deal, he responds with "we mustn't neglect to give water to the one who catches the fish," which seems to indicate he is honor-bound to accept the deal.
From there, the limitation on using Chamber is not entirely understandable story-wise, but it make sense plot-wise. A common problem in sci-fi with any super-advanced technology is that it takes the drama out of the story. A prime example of this is the transporters in Star Trek. If you can simply beam people out of danger, then there is no real tension, danger, or excitement. So almost as soon as the transporters were introduced, the writers realized they had to continually come up with reasons why the transporters would
not work, in order for the plot to have tension and drama. So to with Chamber. If he just nuked the entire pirate main fleet in episode 3, then were exactly does the plot go from there? A slice of life anime at sea for nine episodes?