I haven’t tried it myself, but I would say using the disabledModules is the way to go, as it’s the recommended way of disabling modules in NixOS: docs and it looks like Home Manager supports this attribute as well, see 1, 2, 3.
Something like:
{ config, inputs, pkgs-unstable, modulesPath, ...}: {
disabledModules = [ "${modulesPath}/programs/mise.nix" ];
imports = [ "${inputs.home-manager-unstable}/modules/programs/mise.nix" ];
config = {
programs.mise = {
enable = true;
package = pkgs-unstable.mise;
...
};
};
}
modulesPath is coming from here.