States do have a legitimate interest when it comes to the education of our children, but there are limits and (more importantly) the state has to pass laws to codify that role.
In Texas, there are few laws when it comes to homeschooling. Parents do have a legal right to homeschool their children
To home school legally in Texas, you must follow three state law requirements:
The instruction must be bona fide (i.e., not a sham).
The curriculum must be in visual form (e.g., books, workbooks, video monitor).
The curriculum must include the five basic subjects of reading, spelling, grammar, mathematics, and good citizenship.
These are not unreasonable restrictions (in fact, they make TX just about the most homeschool-friendly state). However, TX didn't go on to grant some state/county agency the power to evaluate compliance with the curricular requirements or whether or not a school is a "sham".
In NC, for instance, we have almost as much freedom... but there is a department that is empowered to audit my school to verify that we are keeping attendance records, evaluating the students at least annually with nationally-normed testing, keep immunization records, and that our home meets fire/safety/etc. standards. They don't get to decide whether or not my kids are making "adequate progress", but they can shut me down if we're not actually schooling.
Without such a law, their attorneys can (and did) simply state that they're in compliance with the state requirements and that the district is not empowered to evaluate that compliance. This actually happens fairly frequently. Some nosey neighbor sees the kids playing outside in the middle of the day when they "should be in school" and reports them for truancy. Then some well-meaning truancy officer treats them like criminals (wants to enter the home and "interview" the kids without the parents present... wants to evaluate the educational materials, nutrition, whatever - to make sure that the kids are safe). The homeschool attorneys send a letter to the school district pointing out that they aren't legally empowered to do what they're doing, and the district's attorney ends up agreeing. The school district apologizes and the HSLDA puts the victory into their next newsletter (often making a larger deal of it than is warranted).
In this case, the family sued the district for constitutional violations. Most of this ruling deals with whether they can bring that lawsuit before the district can handle the claim administratively. It has nothing at all to do with whether or not they think the rapture will interrupt their schooling. That's merely hearsay on the part of a family member who claimed that he heard the children saying that. We don't know that it was said in jest or at all - and it certainly isn't the family's legal position.