Yeah this should be possible using the comment_form_default_fields filter, like so:
apply_filters( 'comment_form_default_fields', $fields );
$fields = array( 'name' => '<section class="form-group">
<input type="text" class="form-control" id="name" placeholder="Your name" />
</section>'
);
Just remember to add any other fields that you want to add into that array too.