It seems that i've not been correctly explaining.
I have successfully joined the computer to the AAD tenant and while using SAML 2.0, but when i want to log in into windows, it asks for username/password, which obviously cannot work as the account uses the SAML 2.0 serveur to authenticate. I have successfully federated the domain, this is not the issue, the issue is that, after joining the computer to the tenant, i cannot login using aad's accounts, the only account that works is the local computer administrator.
I'm not sure if i've been clear, so i'll clear it up, here Azure Active Directory is a Service Provider, the SAML Identity Provider is a standalone, custom SAML 2.0 php implementation. Therefore when logging in, AAD redirects the user (through HTTP) to the IDP for identification.