I think you touch on a really good point. If the federal government was to use its powers like a cudgel to force compliance of the states it also creates a single point of failure if you have a change of government. We should be looking at building legislation at both the federal and state level synergistically.

Tangentially, look at the damage Roe V Wade has caused by being overturned. From how I've understood it the federal (and some state governments) have basically relied on the supreme court decision instead of building proper legislation to protect abortion.

From what I can tell from an admittedly brief search for more information is that if the federal government was to federally criminalise conversion therapy a legal challenge could be mounted by state governments as federal criminal law normally in relation to crime that crosses state borders (i.e. drug trafficking) and might be seen as federal overreach. (Though during my reading apparently the federal government has overridden state laws before; namely overriding Tasmanian sodomy laws so maybe it could be done)

Private school funding on the other hand I'm not as certain about. I don't know if the Act that details how funding for non-government schools is dispensed allows the federal government to place restrictions on funding based on discriminatory practices in these schools. It might be something that needs to be done on a state level.