As far as I know, no, there isn’t any way to deactivate select2 on the fields where it is used. If you want to use regular select field you would need to build a filter to dynamically populate the select field http://www.advancedcustomfields.com/resources/acf_load_field/, there is an example of using this here http://www.advancedcustomfields.com/resources/dynamically-populate-a-select-fields-choices/
Then you’d need to create an acf/save_post action http://www.advancedcustomfields.com/resources/acfsave_post/ to get the value of your select field and update the terms for the post yourself https://codex.wordpress.org/Function_Reference/wp_set_post_terms
