Add a filter the the WooCommerce `wc_reduce_stock_levels` function to not reduce the stock if more then what is in stock is ordered.

woocommerce-override.php

<?php
/**
 * Do not reduce stock if more then what is instock is ordered as all items will be back-ordered/made to order/shipped together, and someone else can have the item instock shipped immediately.
 * TODO: Should probably check if the item allows backordering.
 */
function wccustom_alter_order_item_quantity( $item_qty_ordered, $order, $item ) {
	// Get the product object from the order item object.
	$product = $item->get_product();
	// Some products (variations) can have their stock managed by their parent. Get the correct ID and then product object.
	$product_id_with_stock = $product->get_stock_managed_by_id();
	$product_with_stock = wc_get_product( $product_id_with_stock );
	// Get the product current stock level before the order is processed.
	$product_stock_lvl = $product_with_stock->get_stock_quantity();

	// If the item quantity ordered is greater then the current items stock, all items will be made to order so do not reduce the stock.
	if( $item_qty_ordered > $product_stock_lvl ) {
		$item_qty_ordered = 0;
	}

	return $item_qty_ordered;
}
add_filter( 'woocommerce_order_item_quantity', 'wccustom_alter_order_item_quantity', 10, 3 );