I know this is a little late, but if you still need help or for anyone else looking for similar information.
If you are using ACF in a plugin that will be used on a multisite setup there are a few choices.
1) in your plugin and wherever you are getting values from the options test to see if any value is set and if not then apply the default value.
$option = get_field('my_field', 'options');
if ($options === false) {
$option = 'default value';
}
The above can potentially cause a problem if the field can return false and false is not the default value. In this case you could use the standard WP function get_option()
$default_value = true;
$field_name = 'my_field';
$option_name = 'options_'.$my_field;
$value = get_option($option_name, $default_value');
The other choice it to insert all of the options for the new site when the site is created. This can be done by creating a function that runs on the WP hook wpmu_new_blog. This would be far more complicated. For more information see wpmu_new_blog in the WP Codex and documentation on the ACF update_field() function.
