I've taught in school systems which followed the Alg. 1, Geom, Alg. 2 route, and others which used the Alg. 1, Alg. 2, Geom. order as well.
I think that presenting geometry between algebra 1 and algebra 2 probably goes back to the "old days" where just two years of math was the "norm" for even college-bound students. (I'm talking the 50's here, folks!) Those students who were really "serious" about math would then follow geometry with algebra 2. And this sequence just stuck, though it really makes more sense from a continuity standpoint to do the two years of algebra in sequence. There certainly is more review required to bring an algebra 2 class "up to speed" if the students haven't done all that much algebra for a year.....
In addition, I think it is beneficial for lots of students to acquire a bit more mathematical "maturity" before tackling geometry, which requires a different type of thinking. I know, I know.....many students are capable of handling geometry at the 9th or 10th grade level, but some definitely aren't. Since you are home-schooling, you know more about your child's mathematical maturity than we do, and you also know how much math you plan to present to your child. If you definitely plan for three or more years of secondary math, I don't think you would go wrong to complete the two years of algebra first (in fact, I've recommended this to several of my home-schooling friends).