Check whether the new member has an email address that matches the specified domain and the level they're trying to sign up for is a free level.

allow-fqdn-to-signup.php

<?php
/*
Plugin Name: PMPro e-mail domain check
Plugin URI: http://www.paidmembershipspro.com/wp/pmpro-customizations/
Description: Check if a domain is on the "allow" list for registration
Version: .1
Author: Thomas Sjolshagen @ Stranger Studios <thomas@eighty20results.com>
Author URI: http://www.eighty20results.com/thomas-sjolshagen/
*/

function restrict_email($value)
{
	// skip this check if we haven't got a level yet.
	if (!isset($_REQUEST['level'])) {
		return $value;
	}

	$email = $_REQUEST['bemail'];
	$current_level = isset($_REQUEST['level']) ? intval($_REQUEST['level']) : null;
	$level = pmpro_getLevel($current_level);

	if(true === pmpro_isLevelFree($level) && false === is_valid($email))
	{
		global $pmpro_msg, $pmpro_msgt;

		//TODO: Set the error text to be whatever you want it to be:
		$pmpro_msg = "Please enter a valid .edu address";
		$pmpro_msgt = "pmpro_error";
		$value = false;
	}

	return $value;
}
add_filter('pmpro_registration_checks','restrict_email', 10, 1);

function is_valid($email)
{
	$test_domain = getDomainFromEmail($email);
	$valid_domains = array("*.edu");

	foreach($valid_domains as $v_domain)
	{
		$components = explode(".", $v_domain);

		if($components[0] == "*")
		{
			unset($components[0]);
			$v_domain = implode('.', $components);
		}

		if((stripos($test_domain, $v_domain) !== false)) {
			return true;
		}
	}

	// The domain specified in the email address is one of the valid ones.
	return false;
}

//Taken from: http://www.bitrepository.com/how-to-extract-domain-name-from-an-e-mail-address-string.html
function getDomainFromEmail($email)
{
	// Get the data after the @ sign
	$domain = substr(strrchr($email, "@"), 1);

	return $domain;
}