Elena knew that Silas couldn't be all bad. She knew that because he could love Amara the way that he did. Nobody who could love could be all bad. But Elena knew that some who could love could still be pretty bad. She and Damon weren't perfect, none of them were. It was easy to paint them in the role of the villain or the hero depending on the week. Maybe they were neither, maybe nobody was.
All Elena knew was that Salem was their safe place, where they could be happy and together. It wasn't perfect. Things like devastating magical tornados happened and Stefan had some strange link to the coven of witches controlling the town. So it wasn't all great but Elena liked it better than being in a coma. She liked it better than Damon and Bonnie being dead. That was the worst. She couldn't imagine anything that would be more painful.
She didn't want all of that to be threatened all because the original doppelgangers were there. Life was going to be long for Elena and she didn't want to hold grudges. The one exception to that rule was Katherine. Elena was all out of chances to give that soulless bitch.
She wanted to push the issue. Did Elena get to live now or indefinitely? And what about her friends? Was Silas still a homicidal maniac even with Amara in his arms? And how would Amara even respond to that side of Silas. Just because she hoped for the best didn't mean that she wasn't prepared for the worst. And well, when she inevitably wasn't prepared for the worst, Damon was.
Now wasn't the time. They were finally back together and now that she was with Silas, he could do the rescuing. Elena would approach him later, after he had some time with her.
"Can I go?" she asked. "I think you have her now. I just saw her out in the hallway and she looked upset so I followed her."