You’ve practically got the solution in the code 😉
Notice that the entire content of the first post is visilbe, but for the rest only the excerpt displays. That’s from this (after tidying):
<?php
if( $wp_query->current_post == 0 && !is_paged() ) {
the_content();
} else {
the_excerpt();
}
?>
So let’s just apply that logic to the thumbnail part:
<?php if( $wp_query->current_post != 0 || !is_paged() ) { ?>
<div class="excerpt-thumb">
<a href="https://wordpress.stackexchange.com/questions/121776/<?php the_permalink(); ?>" title="<?php printf( esc_attr__( 'Permalink to %s', 'twentyeleven' ), the_title_attribute( 'echo=0' ) ); ?>" rel="bookmark">
<?php the_post_thumbnail('excerpt-thumbnail', 'class=alignleft'); ?>
</a>
</div>
<?php } ?>