From your bare-metal management machine, you can run ~/sovereign-stack/uninstall.sh. This will remove the ss-mgmt VM on your management machine. Under no circumstances does uninstall.sh delete any directories. Only VMs and logical networks.
If you want to go a bit further, you can pass the --purge flag to uninstall.sh and your incus storage disk and other artifacts will be removed. In addition, the incus apt package will be removed from your management machine.
Also note that running uninstall.sh only affects the management machine. If you have any deployments running on remote cluster hosts and you want to purge all Sovereign Stack deployments from it, you would use ss-reset from WITHIN the SSME first.
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