I also have had some issues with many wp-cron processes running and causing CPU throttling.
As I knew which plugin was running, rather than disabling wp-cron on wp-config.php (I am not brave enough .), I came up with a few lines of code using API_transient that make the trick.
$prefix = .... // something to help you searching your stuff on wp_options table
$name = ..... // whatever identifies your function
$mins = .... // maximum frequency
$trname = substr( $prefix . sprintf( "%u", crc32($name)), 0, 45 );
if( get_transient($trname) )
return "-- not yet";
set_transient( $trname, date('c'), $mins*60 );
// your program ....
