I ran into the same problem of an array of objects inside of an object that I wanted to clone all pointing to the same objects. However, I agreed that serializing the data was not the answer. It was relatively simple, really:
public function __clone() {
foreach ($this->varName as &$a) {
foreach ($a as &$b) {
$b = clone $b;
}
}
}
Note, that I was working with a multi-dimensional array and I was not using the Key=>Value pair system, but basically, the point is that if you use foreach, you need to specify that the copied data is to be accessed by reference.