Although after detonating the Power Station Beacon you can tackle the remaining eight Beacons in any order you wish, it is highly recommended that you detonate the remaining Beacons in the order they are presented in this guide.
Crackdown 2 is an open world game, but some parts of the city are rougher than others. As such, you'll want to take on the Beacons in the order the game instructs you to via the flashing Absorption Unit icons on your map and tracker.
Once you clear all of the Beacons in Hope Springs, your Agent will be better equipped to survive Green Bay and then Unity Heights. Later Beacon deployment areas require a skilled Agent with powerful weapons, so it's best to work your way up.