I'm trying to read your question correctly: Do you mean you now have 1 site that has a non-Meraki VPN to Azure and you want to add a second site that also talks to Azure but not to each other? If it is true, allow me to explain below: The hub and spoke settings indeed apply to AutoVPN only (that means Meraki to Meraki in the same org). You always need at least one hub in your network and I believe if you set the new site to spoke you'll need to select at least one hub. So indeed they will connect via AutoVPN. Or if you configure them both as hub then it will yield the same result. So you have two ways to block communications between the two sites: 1) You configure both sites in their own org. Do know this will also split your licensing, so you'll need separate orders if you do a renewal or something. 2) You can keep them in a hub/spoke config but you'll need to add some rules to the site-to-site VPN outbound firewall ruleset. Just put denies between both networks ( maybe use a supernet if the network design is solid ) and make sure you have an allow any below it so you can reach all the rest. Or only allow the Azure subnets as destination. These rules will apply to both networks.
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