The last days of the Prothian Empire they sent a warning about the reapers to all the empire for future races to find, embedded in the warning was the location of the 'Conduit' the back door to the Citadel, unfortunately over the 50.000 years the information became fragmented, 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 vermire 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 Realay.
Sovereign didn't want the beacon destroyed, it just wanted Saren to use it to sneak into the Citadel without interference and override the old Prothian tampering that was stopping it 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.
