While I agree, the Normandy being able to land in the middle of all that feels very odd, I think it can be (barely) justified. Right at the moment, Harbinger was too busy keeping everyone away from the beam, so there was no reason for it to attack Normandy, unless it posed a direct threat (like say, if it took a pot shot with the thanix cannons.) It might also be worth noting that other wounded soldiers were being brought up the ramp, so it's not as if it landed *just* to pick up Shepard's squadmates.
It still could have been handled better though. Like say a mention in the mission briefing that it'd be on station for med-evac. The theory being that it's the only ship small enough to land in close and tough enough to take a direct hit from a reaper beam weapon and live.
Of course, just about everything from killing Kai Leng onwards could have been handled better. I'm also still having a hard time figuring out how the EC managed to take up more memory than LotSB. I was half expecting to see new additions in the for of support based on past decisions (rachni, elcor, Jack's students etc.) Until the beam, I was getting a little worried that the DLC hadn't installed properly.