Merely having poly-markdown installed shouldn't cause it to replace markdown-mode. That should only happen if (require 'poly-markdown) actually runs. But because the addition to auto-mode-alist is marked autoload, just installing poly-markdown causes it to effectively replace markdown-mode:
;;;###autoload
(add-to-list 'auto-mode-alist '("\\.md\\'" . poly-markdown-mode))
The ;;;###autoload part should be removed.