While I can see the ideas that an extremely faithful Christian may have (and forgive me if I offend you in this post--not my intent, by any means) with this episode. However, MITM isn't geared towards the politically correct audience. This is not the first time that the show has tackled some type of controversial issue.
Judging from a religious thread we had here a few months ago, many MITM fans aren't avidly into religion, and have trouble understanding why people have so many problems with other people's problems. That's not to say that people who disagree with that idea shouldn't watch MITM. If everyone stopped watching if the show marginally insulted them, there wouldn't be any viewers left. From the top of my head, the show has tackled racism, sexuality, disability, stereotypes, smartness, cliques, issues in the family, justness of law, the meaning of a holiday, ethics, the afterlife, teenage depression, pregnancy, and supersition. That's quite a list by any stretch. Are dumb people offended by Malcolm's IQ? Are judges offended by episodes like Jury Duty? Are people with divorced parents offended by episodes like Krelboyne Picnic and Family Reunion and Hal's Christmas Gift offended?
MITM has dealed with a lot of very controversial issues, but that's what makes the show special. Every episode isn't politically correct. I mean, in the first episode, Lois walked around the house with her boobs sticking out while Hal was shaved naked. That's not exactly conservative. And I think that Daycare was just another way of viewing this issue. Every time the series deals with a controversial issue, it takes some type of standpoint. And that's just the standpoint that it took in this ep. it doesn't mean it's right or wrong; it's just the reasoning of the writers.
Furthermore, as you said, that scene was through Dewey's eyes. A lot fo the series is through the eyes of a teenage boy, which may substantially change the viewpoint. The best example of this that isn't controversial is in Smunday when Lois rises out of bed--of course, that's what Malcolm sees, not what really heppens. And this is just Dewey's ideas of religion.