Well, it depends. In principle, yes. AxCrypt works on files that are accessible on your local computer. I’m not quite sure how Google works with different accounts in the same computer, but if you can get the Google desktop app to synchronize them, you can then encrypt them with AxCrypt.
Otherwise, as you say, download them, encrypt them, delete them on Drive and upload them.
In any case, when doing things like this, do ensure good backups!