If you do delete vpn ipsec and commit, it will fail because the ipsec-settings.py scripts will want to restart strongswan whether it should be running or not.
vyos@vyos-test-2# delete vpn ipsec [edit] vyos@vyos-test-2# commit [ vpn ] VPN configuration error: IPSec process did not start. [[vpn]] failed Commit failed [edit]