I don't believe there is a tool "right now" that will allow you to synchronise accounts from a Samba DC to Azure Active Directory. You should be able to set up your spare Windows Server as a secondary Domain Controller and then synchronise from that using Azure AD Connect, though.
Another option - albeit a heavyweight one - might be to go the Federation route and use your own SAML authentication server(s) to authenticate access to Office 365. This is not for the faint-hearted; I've not yet managed to get Microsoft's Federation-based authentication to work with exclusively Microsoft software in the loop, so I suspect you would be embarking on a voyage of discovery without any knowledge that the edge of the world really wasn't a gigantic waterfall...
In practical terms you might get a more hands-on answer over on Server Fault.