From what I read about the Mass Effect 2 DLC Arrival, Shepard destroyed the Alpha Relay because this was going to be an entry point of the Reaper invasion, so destroying it delayed the invasion.
Even though the Citadel has a mass relay inside it, there is a smaller one in the Widow Nebula which is used to reach Citadel for most beings. And we see that Sovereign uses the external relay without some sort of overload to the relay. (Sovereign and a Geth Armada also used it along with the Alliance Armada).
Why did the Reapers need the Citadel to be a mass relay when they could have just used the nearby one and then block communications to prevent any warning from getting out?