Starting from v3.1, tmux looks for ~/.config/tmux/tmux.conf in addition to traditional ~/.tmux.conf for configuration files. You can use -f option to specify an alternative configuration file and since your ~/.tmux.conf has right context, you will not get an error.
BTW, how do you start tmux? I start it from terminal manually and it has SELinux context of unconfined_u:unconfined_r:unconfined_t so it can access ~/.config/tmux/tmux.conf as well as ~/.tmux.conf without any error.