It's not even close to the only explanation. You did a fine job of spelling out how the judge probably meant "homophobic" to be understood:
"make sure that there is nothing in the upbringing or teaching that the minor child is exposed to that can be considered poisonous to Dr. McLeod."
The only thing missing from this is a reason for the judge to specifically mention "homophobic," and "Christian teaching."
I believe we are both sufficiently well-versed in Scripture to figure out which particular "Christian teachings" he has in mind. The only remaining question is whether he's an anti-Christian activist, or whether he's addressing a very specific allegation made in this case.
You're claiming the former, and I think it's much more reasonable to believe the latter.
If he's addressing a specific allegation, I think we can also reasonably derive what the allegation is: that Ms. Clark is telling the little girl that Ms. McLeod is going to hell because she's a lesbian; and probably that Ms. Mcleod is evil, and that Christians shouldn't consort with evil people; and that if she (the girl) doesn't want to be evil, then she'll stay away from Ms. McLeod.
Now -- just suppose I'm right, and that Ms. Clark is using "Christian teaching" to poison the little girl against Ms. McLeod. Do you think it is morally and theologically correct to use Christian teaching in that manner?
I think it's profoundly wrong to misuse Scripture in that way. From my perspective, the judge (whether he meant to or not) could very well be protecting the spirit of Scripture against a misuse of the letter of Scripture.
What you don't seem to be taking into account is how case law works in this country. Let's forget, for a moment, that Ms. Clark was a lesbian herself and is very likely to have compassion on those still trapped in the lifestyle (based on my personal experience with ex-gays - they are greatful for the compassionate ministry that helped them and very much want to help others still trapped in the lifestyle). Even if Ms. Clark was doing what you say, by mentioning religion in the ruling, the judge creates a precedent that can be used against any religious teaching that can create a negative impression against any person. If the judge had limited the ruling as I suggested it could only be applied to Ms. Clark and Ms. McLeod. He set a precedent, and I have to believe he knew what he was doing.
Shalom.