Drupal - Revert a Feature Component programmatically
Here are a few thoughts though on resetting your features programmatically or as add-on install scripts.
You could use Drush to reset the Feature:
drush features-revert [feature name]
Another thought would be to use features_revert() during the install process:
features_revert(array('module' => array('component')));
The Strongarm module could be useful as well to force your Feature to retain its default state I think.
I have to agree with @Letharion in his comment on your OP. I would want to know that other important things aren't being mistakenly modified during the install process.
You can revert a single features module with features_revert_module().
features_revert_module('my_feature');
Revert ALL components in feature
$feature = features_get_features('my_feature_machine_name');
$components = array_keys($feature->info['features']);
features_revert(array('my_feature_machine_name' => $components));