She couldn't stay with him.
Aria knew that the moment they'd kissed after he told her 'I know a broken soul when I see one.'
He had offered to let her stay at his house for the night, and then promised to help her get back on her feet. Granted, Aria didn't want to make trouble for him, but he eventually convinced her that it was in her best interest.
But it wouldn't end there. A time would come when Flash would ask her to come back to Canterlot High, just to get an education, maybe make new friends. And then he'd ask her to try being friends with the Rainbooms. She knew he wasn't manipulating her, but he would keep encouraging her to do so, and after all she did to hurt everyone at the school, she couldn't face them.
She hated herself for being a coward, but running into the Rainbooms again would only bring pain to Flash, and to Twilight, if she came back, and she couldn't do that to either of them.
She woke just before dawn with her plan already set. Gathering up her things, including a spare leather jacket that Flash insisted she take, she snuck to the room across from hers, where Flash slept.
Aria had no plans for world domination, nor to seize revenge. She would travel to a nearby town, maybe get herself into a music showcase, where she could show off her talent reborn, and get some money in. After raising enough, she'd move elsewhere, mostly so that Flash wouldn't follow her, try to bring her back. She would become stronger than ever before, but only to have audiences praising her willingly. Real, genuine adoration would be hers.
She had a gut-feeling this plan meant she would never see Flash again. But if it meant he would be saved from losing his reputation by hanging out with a Siren, then the price was acceptable. Because of this, she needed to see him one last time.
Aria walked beside his bed, staring off into space. She had nothing left, yet he gave her his compassion, and a second chance to live. That was a debt she could never repay. Yet, it would be cruel to leave without giving him something to at least remember her by.
She had to leave. Now. Or else she'd never get the chance. Once she placed her gift on the desk by his window, she darted out of the room. Maybe one day, he'd forgive her for this. Maybe he'd understand that she couldn't stay. But she prayed that he would never come after her. No monster was worth hunting where she was going.
Goodbye. And thank you for believing in me.
When Flash would awaken an hour later for school, he would find Aria's gift, and treasure it above all his other possessions.
Because Aria's star-cluster hair clips were so precious to her, letting them go would set her free from the sins of her past.