The other couple for various reasons.
First though I'll comment on the Scientologist couple. They did what every other religious group does - proselytize. Please keep in mind that Scientologists are basically brainwashed to believe that Scientology is the only way to save the world. They think they're doing the right thing. As a critic of the Church of Scientology, I hold no malice towards your average Scientologist.
Most of them are decent people who have been gulled into following a bad path. The organization itself and those who live at the top of it and are aware of the scam and work to keep it going, mistreating both critics and their own members, are the ones that should be hated if anyone is to be hated. The worst thing this Scientologist couple did was proselytize to a kid in the ignorant belief that they would be helping him - they shouldn't have been preaching their religion to someone else's kid, but at the very least their intentions were good.
Now, as to why the other couple is worse.
The first thing they did wrong was how they reacted to their child's interest in Scientology. They reacted in an angry fashion to their child's interests, destroying the materials he worked hard to gather and forcing him to watch propaganda films. This type of behavior could traumatize this kid, and at the very least he'll be less inclined to involve his parents in any of his future interests. Should any of his future interests be of a bad sort, his parents won't find out about it if that's the case. It also might make him resent them to the point that he'll continue to pursue Scientology anyways, which could result in him becoming a member and disconnecting from them when he's an adult.
The proper course of action would be to have a nice sit down with him, and to explain calmly and rationally why Scientology is bad and suggest that he look into what the critics are saying - in fact the biggest critics of Scientology all suggest that anyone who isn't in the know look at both sides of the story before making a decision. They'll happily link to the Scientology's website. By doing so they would encourage him to do research before making his decision, in not only Scientology but any future interests he has.
The second thing they did wrong was treat the Scientologists the way they did. The Church of Scientology makes it clear in their fair game policy that it's okay to lie to, harass, and destroy any critic of Scientology. This is one of the biggest things critics of Scientology have against the CoS. So if you think the Scientologist couple is worse, I ask you to ask yourself why you think it's acceptable that the other couple did the exact same thing that the Church of Scientology does. Frankly I don't see it as acceptable, I see it as hypocritical.
The worst part of using harassment against cultists is that it is the worst possible thing you can do to harm the cult. Why? Because it only makes the harassed more insulated into the cult. Believe it or not there are a good number of Scientologists who would like to leave the cult, but they don't. The biggest reason for this is that their family, their friends, and everything they have become accustomed to in their daily lives may be lost if they leave. The fear of losing everyone they know is so scary that they'll put up with the pain of staying. Harassing them would only increase their fear of the world outside the cult, and it may even make them more likely to keep believing what the cult says.
The best way I can think of for the other couple to handle the Scientologists would be to go to them directly, state that they disagree with their beliefs but that they also respect their right to believe in them, and inform them that it's generally considered rude to proselytize to other people's children and that it could cause problems down the road with the parents of anyone they did it to. Then if the Scientologists apologize, invite them over for dinner one night. That's right, invite them over for dinner. Make friends with them. Be polite to them. Why? Because as I said earlier, many people who want to leave cults don't because the world outside the cult doesn't hold many apparent prospects for them. By giving them friendship outside the cult, you give them something outside the cult to look forward to if they want to leave. If they refuse to stop proselytizing, then getting people to ignore them would be alright, but not harassment because that's just dead wrong.
To further drive home my points, I'm going to rewrite the story a bit:
A Scientologist Buddhist couple moves into a neighborhood. They at one point hand a pamphlet on Scientology Buddhismto one of the Christian neighbors' kids. He gets interested and starts talking to his parents about how he wants to get involved in Scientology Buddhism. The outraged parents confiscate and destroy any material he has on Scientology Buddhism and force him to observe anti-ScientologyBuddhism propaganda. Then they let the rest of the neighborhood know, and a vicious campaign of shunning and harassment happens to the Scientologists Buddhists. It gets so bad they are forced to leave the neighborhood.
Now, I don't see how indoctrinating the kid and harassing the neighbors for having different beliefs is acceptable in this scenario, so why the hell would it be okay in the original one?