I don't see any reason why she couldn't take them again, if she struggled with them. Algebra and Geometry are high school math for most kids, after all. I actually took Algebra twice in high school despite passing it the first time, because I didn't feel like I understood the "whys" of it.
DS11 (2e - ASD) took the second half of Algebra 1 last year with his e-school, and is taking Geometry this year as a full-time e-schooler, but it's a Colorado-specific online school, so I probably can't recommend it to you. But they do use some Khan Academy videos in their classes, so that might help. Other than that, I don't know about spectrum-related math classes.
Has she done Dragonbox? They are nice as a game-way to get across the concepts of algebra, and I heard they were putting out a geometry one as well. DS and DD both liked the algebra one.