Yes, there's instruction in alternative school, but there are also huge negative consequences for kids. At least where I live alternative school goes on the transcript, creating implications for college admissions. Alternative schools also generally don't offer the same range of courses, so kids lose their electives, often lose a year's progress in their foreign language, etc . . . Finally, kids at alternative schools are at high risk for drop out.
For a kid who is clearly floundering and falling apart in their home school, or whose behavior is so unsafe that they can't be kept in their home school, then yes I can see trying alternative school as an option. But for a single incident of school skipping, or for writing 3 letters on the wall with a marker, I think it's overboard. I agree with you that suspension is a bad idea, especially for offenses that aren't violent and don't involve illegal substances, but there are other options that keep kids in school and have them fix their mistake. Alternative school carries too many risks for it to be a first round consequences, in my opinion.