Change workflow default state with hook_form_alter()
It seems your implementation of hook_form_alter() runs before the one provided by the Workflow module. Implement hook_module_implements_alter() to change the order in which implementations of hook_form_alter() are executed. Alternatively, give your module a higher weight than the Workflow has.

Beware that this approach does not work for changing the order of implementations of hook_form_FORM_ID_alter() specifically. Implementations of hook_form_FORM_ID_alter() are always executed in the same order as those of hook_form_alter(). This is due to the way how drupal_prepare_form() calls drupal_alter().