To remove aspects from a node, use the NodesApi.updateNode method. The way you do this is described in Updating Metadata for a Folder or File.
Removing an aspect from a node is similar to how you add a “marker” aspect. You first get the list of aspects currently applied to the node. Then you remove the aspect from the list. And finally you use an update node call with the updated aspect list.
For more information about this ReST API endpoint, see Remove Aspects From a Folder or File.