He didn't attempt to actually protect Stellar first dumping her on Neo and then standing there as Kira disabled destroy.

A) He HAD to give Stellar to Neo, or she would have died, plain and simple. I know it sucks, but Shinn could either give her to Neo and hope beyond reason that Neo didn't get her killed, or just watch helplessly as a loved one died right next to him. Again. Unless you're thinking that ZAFT would miraculously come up with a way to treat her with limited specialty equipment an a war vessel.

B) He was still trying to calm Stellar down. He was focused on her and her mental state, not on what Freedom was doing. If Freedom was not in Stellar's line of vision, she would not have fired her cannons, and Freedom wouldn't have needed to disable Destroy to save Shinn. I'm not saying it's Freedom's fault exactly, as Kira didn't know exactly who and what was going on, but saying that it in any way Shinn's fault is pure fiction. He had her calmed down. She had stopped firing, because of Shinn, and if given some more time, he prolly could have coaxed her out.