They *are* doing the basic housekeeping. What do you think this announcement is, if not exactly that? AUR is very clearly documented as user-submitted, and automatic installs from it are heavily discouraged by the maintainers for this reason. Malware aside, there is very little quality control, and a poorly made AUR has the potential to break the system pretty badly. (Though, in my experience, most of the useful AUR packages are trivial to remove if something goes wrong.)

The officially maintained repositories (which are part of a default installation) were not affected. Users need to go somewhat out of their way to use an AUR.

The definition files are all plain text and not especially complicated. It's not too difficult to glance at the file before doing an install to get a basic idea of what it's about to do, just like you should do when running a random shell script or cloning a random git repo. Indeed, most AURs are implemented by cloning an upstream git repo and configuring it so it can be built. The same basic threat model applies: Do you trust the install script? Do you trust the upstream URL whose code it is about to compile?