Typically you can use handlers to update conf files (such as the services/data/transforms endpoint for transforms.conf), but macros are an exception. The Splunk REST API does not offer any dedicated handlers for macros.
You can use the /acl endpoint to change permissions (as you discovered), or you can use the /properties or /configs handlers to manipulate macros.conf files directly: http://docs.splunk.com/Documentation/Splunk/latest/RESTREF/RESTconf
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