In order to configure Alejandra in Doom Emacs just use the following:
(after! nix-mode
(set-formatter! 'alejandra '("alejandra" "--quiet") :modes '(nix-mode)))
If you've enabled formatting via LSP in Nix, you might also need to add the following:
(setq-hook! 'nix-mode-hook +format-with-lsp nil)