Yes you can set primary dns on Linux and secondary on windows. We are already using it but we have 3 dns servers,
1st primary Dns = Linux
2nd Dns = Linux
3rd Dns = MS-dns
When you use multiple dns roles with HC especially windows and linux combination then make sure that both servers in same network. If machine as in different network and not running directly with Public IP then zone transfer request from primary to secondary would fail.