Of course you can migrate a running instance from a disk-based datastore to an S3 Datastore. Next to reconfiguration you also have to copy all the local binaries to S3 first before you start AEM with the new configuration.
For details see the parameters for crx2oak (Using the CRX2Oak Migration Tool ), especially the --src-datastore and the --s3config parameters.
Regarding GC on S3: That's straight forward and nothing special with it. In your case you can use the documentation for GC on shared datastore: Configuring node stores and data stores in AEM 6
Jörg