Miss Emily was on their side or not?

Hailsham was more of a social experiment, in that the clones were raised and nurtured like ordinary children, playing sport, producing art and poetry, learning how people behave in the outside world. The point of all this was to see if the clones had souls, but it was also an improvement on the way clones had been treated before Hailsham had opened. The movie doesn't explain it as thoroughly, but in the novel, when Kathy and Tommy go to see Miss Emily and Madame Marie-Claude, Miss Emily said:

"But in the end we were obliged to close, and today there's hardly a trace of the work we did. You won't find anything like Hailsham anywhere in the country now. All you'll find, as ever, are those vast government "homes", and even if they're somewhat better than they once were, let me tell you, my dears, you'd not sleep for days if you saw what still goes on in some of those places. And as for Marie-Claude and me, here we are, we've retreated to this house, and upstairs we have a mountain of your work. That's what we have to remind you of what we did. We have a mountain of debt too, though that's not nearly so welcome. And the memories, I suppose, of all of you. And the knowledge that we've given you better lives than you would have had otherwise."

"She had the makings of an excellent guardian. But what she was wanting to do, it was too theoretical. We had run Hailsham for many years, we had a sense of what could work, what was best for the students in the long run, beyond Hailsham. Lucy Wainright was idealistic, nothing wrong with that. But she had no grasp of practicalities. You see, we were able to give you something, something which even now no one will ever take from you, and we were able to do that principally by sheltering you. Hailsham would not have been Hailsham if we hadn't. Very well, sometimes that meant we kept things from you, lied to you. Yes, in many ways we fooled you. I suppose you could even call it that. But we sheltered you during those years, and we gave you your childhoods. Lucy was well-meaning enough. But if she'd had her way, your happiness at Hailsham would have been shattered. Look at you both now! I'm so proud to see you both. You built your lives on what we gave you. You wouldn't be who you are today if we'd not protected you. You wouldn't have become absorbed in your lessons, you wouldn't have lost yourselves in your art and your writing. Why should you have done, knowing what lay in store for each of you? You would have told us it was all pointless, and how could we have argued with you? So she had to go."