You may declare any of your fleets to be "at peace." When you so declare a fleet, it will remain "at peace" until you declare otherwise.
Declaring a fleet "at peace" turns off a few otherwise automatic behaviors.
A fleet "at peace" will not capture worlds or empty fleet keys, nor will it force empty fleet keys to go neutral. A fleet "at peace" will not frighten an opponent's population away from industry. A Raider's "at peace" fleets will not perform the three-to-one Commandeer. If you are an Missionary, your "at peace" fleets will not make converts on the world below.
That's all that "at peace" means. An "at peace" fleet may still attack, or even drop a PBB, if ordered to do so. An "at peace" fleet will even still ambush fire any passing enemy fleets.
Don't be misled into thinking an enemy is necessarily waving a flag of truce simply because you see that his or her fleets are "at peace."