If a discipline was compiled in separate books only after the earliest generations, its later date alone does not establish that every part of it is an unacceptable religious innovation. We must distinguish the content of belief from the method used to explain or organize it.
Collecting relevant verses, reports and arguments under a topic can be an educational procedure. Introducing an unsupported creedal claim through that procedure would require separate scrutiny.
Historical criticisms of certain styles of kalām are not the same as a proof that all later scholarly organization is illegitimate. Sound analysis distinguishes useful method from mistaken content.