However, I need to keep the NTLM for my users.
Is there a way to keep the NTLM for users but deactivate only the one for CMIS ?
I am afraid there is not. Either you have HTTP SSO enabled or not. There currently is no differentiation between different HTTP-based APIs unless you manually rewire the authentication filter mapping.
May you confirm your Alfresco version ?
Thanks for your comments, my Alfresco version is 5.2.
I'm not sure to understand how to manually rewire the authentication filter mapping, may I ask you further informations ?
My remarks should not be construed as an advice on what to do. They were merely meant to explain that this is not supported, and you'd need to change a central piece of out-of-the-box configuration/implementation.
If you'd really wanted to go in that direction, you would have to change the servlet filter mappings inside the web.xml file bundled in the Alfresco Repository WAR. To do that, you should be familiar with the servlets specification, what the various Alfresco filters do and how they interact with other components of Alfresco. Again, this is not something that I advice or recommend.