MinFilterIterator.php

<?php
// Reduced to the minimum
class ThumbnailFilter extends FilterIterator
{
	private $wp_query;
 
	public function __construct( Iterator $iterator, WP_Query $wp_query )
	{
		NULL === $this->wp_query AND $this->wp_query = $wp_query;
		parent::__construct( $iterator );
	}
 
	public function accept()
	{
		$this->wp_query->the_post();
 		$this->wp_query->current_post === $this->wp_query->query_vars['posts_per_page'] -1
			AND $this->wp_query->rewind_posts();
 
		return $this->wp_query->have_posts() AND $this->deny();
	}
 
	public function deny()
	{
		return ! has_post_thumbnail( $this->current()->ID );
	}
}

WP_QueryFilterIterator.php

<?php
/**
 * Plugin Name: (#130009) Merge Two Queries
 * Description: "Merges" two queries by using a <code>RecursiveFilterIterator</code> to divide one main query into two queries
 * Plugin URl:  http://wordpress.stackexchange.com/questions/130009/how-to-merge-two-queries-together
 */

class ThumbnailFilter extends FilterIterator implements Countable
{
	private $wp_query;

	private $allowed;

	private $counter = 0;

	public function __construct( Iterator $iterator, WP_Query $wp_query )
	{
		NULL === $this->wp_query AND $this->wp_query = $wp_query;

		// Save some processing time by saving it once
		NULL === $this->allowed
			AND $this->allowed = $this->wp_query->have_posts();

		parent::__construct( $iterator );
	}

	public function accept()
	{
		if (
			! $this->allowed
			OR ! $this->current() instanceof WP_Post
		)
			return FALSE;

		// Switch index, Setup post data, etc.
		$this->wp_query->the_post();

		// Last WP_Post reached: Setup WP_Query for next loop
		$this->wp_query->current_post === $this->wp_query->query_vars['posts_per_page'] -1
			AND $this->wp_query->rewind_posts();

		// Doesn't meet criteria? Abort.
		if ( $this->deny() )
			return FALSE;

		$this->counter++;
		return TRUE;
	}

	public function deny()
	{
		return ! has_post_thumbnail( $this->current()->ID );
	}

	public function count()
	{
		return $this->counter;
	}
}

class NoThumbnailFilter extends ThumbnailFilter
{
	public function deny()
	{
		return has_post_thumbnail( $this->current()->ID );
	}
}

add_action( 'loop_start', 'wpse130009Query' );
function wpse130009Query()
{
	// Only need to remove this callback for the current test
	// Else we'd infinitely nest this callback as WP_Query::the_post()
	// calls the 'loop_start' filter.
	remove_action( current_filter(), __FUNCTION__ );

	global $wp_query;

	echo number_format_i18n( $wp_query->found_posts );

	$arrayObj = new ArrayObject( $wp_query->get_posts() );
	$primaryQuery = new ThumbnailFilter( $arrayObj->getIterator(), $wp_query );
	$secondaryQuery = new NoThumbnailFilter( $arrayObj->getIterator(), $wp_query );

	foreach ( $primaryQuery as $post )
	{
		var_dump( get_the_ID() );
	}

	foreach ( $secondaryQuery as $post )
	{
		var_dump( get_the_ID() );
	}
}