You can use PHP in your functions.php file to insert inline JavaScript (including jQuery) using WordPress hooks.
In your example, you could use the admin_print_scripts-post.php
action hook to print your inline jQuery like so:
function wpse_admin_print_scripts_edit() {
echo "<script>var limit = 2;' .
'jQuery('input.single-checkbox').on('change', function(evt) {' .
'if(jQuery('input.single-checkbox:checked').length > limit) {' .
'this.checked = false;' .
'}' .
'});</script>";
}
add_action( 'admin_print_scripts-post.php', 'wpse_admin_print_scripts_edit' );