During the last days of the Prothean Empire, they sent a warning about the Reapers to all of the empire for future races to find. Embedded in the warning was the location of the 'Conduit': the back door to the Citadel. Unfortunately, the information became fragmented over the 50,000 years, and the information on the beacon on Eden Prime was damaged. Gaining that bit of the information brought them 'one step closer to finding the Conduit'. The second beacon on Virmire filled in the missing gaps, or vice-versa. The Cypher from the Thorian was needed to understand it all, and then the Rachni Queen was needed for the new location of the Mu Relay.
Sovereign didn't want the beaconConduit destroyed, it just wanted Saren to use it to sneak into the Citadel without interference and override the old Prothean tampering that was stopping it from controlling the Citadel. To help, Sovereign used the Geth to create a distraction. Otherwise Sovereign would have had to have fought the whole Council fleet to get to the Citadel. Then Saren would have had to fight his way from the docks all the way to the Spire. If he'd died along the way the whole attack would have been for nothing and alerted the Council to the existence of the Reapers.