Lily might have known the truth, but that didn't change the fact that she loved Sirius like a brother. He was Harry's godfather and regardless of his reasons, he had no way of knowing what would happen. Lily could be impetuous and unyielding, but she could, on occasion see reason. No, Lily chose to feel anger toward all those who willingly left Harry alone in a wizardless world for nearly 11 years. She might not have known the exact abuses her boy suffered at her sister's hands, but she certainly knew he had not been loved and cared for like he deserved. For that alone, Lily had "bigger" things to be mad about.
When she heard the familiar voice, she slipped out of the bathroom, her towel firmly around her. "Oy, come in, but be warned I was in the shower, love!" She tightened her towel, making sure he couldn't see a thing.