I've heard it claimed (by BioWare? In the EC? I forget) that the relays really are just damaged and eventually they get fixed. I can see this happening in Control and Synthesis because the Reapers are still around and (especially in Control) you can get them to help repair the relays.
They've already said a couple of times that ME3 was it for Shepard too.
Edit: Too slow. Pretty sure in the Control ending they fixed them too. I mean.. you control them, The Reapers will do whatever the hell you want.
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