As far I know, CMIS provides a very basic management of Alfresco permissions (cmis:read and cmis:write). But surely, you can set up a content rule that may be triggered from CMIS for disabling inheritance in case of folder creation.
Yes, first create a content rule in rootPath folder of your application in the repository. This rule will apply over all content created of type Folder (recursively) and runs a JS-API script placed in /Data Dictionary/Scripts. The script should do something like this: