Use pmpro_levels_array filter to hide specific (in this case free) levels.

my_pmpro_levels_array.php

function my_pmpro_levels_array($levels)
{
	$newlevels = array();
 
	foreach($levels as $level)
	{
		if(!pmpro_isLevelFree($level))
			$newlevels[] = $level;
	}
 
	return $newlevels;
}
add_filter("pmpro_levels_array", "my_pmpro_levels_array");