1. The ponification serum was made with Equestrian magic and nanotechnology, that same nanotechnology could be used to modify the human body and make it immune to the effects of magic.

2. This one is slightly more improbable, a blood transfusion with an alicorn of similar blood type.

3. Gene therapy.

In order to be able to think about these matters, you need to actually read the relevant stories. Read the relevant stories before you post nonsense.

1. The ponification serum was made with Equestrian magic and nanotechnology, that same nanotechnology could be used to modify the human body and make it immune to the effects of magic.

Equestrian "magic" (not really magic) stops quantum effects. This is because absolute knowledge must exist in order to, say, transform an orange into a bird (seen in the canon show) or for Twilight to transform her parents into plants (the pilot episode of the show). Quantum indeterminacy is the opposite of absolute knowledge. All earth life depends on quantum effects to function. Ending quantum effects would kill earth life instantly. Nanotechnology would not, and literally cannot, change this in any way. Also, nanotechnology itself is made of atoms, and atoms depend on quantum effects to exist at all.

2. This one is slightly more improbable, a blood transfusion with an alicorn of similar blood type.

Ponification serum is literally made from the blood of either Celestia or Luna. That is where it comes from. That is the fluid that runs the nanomachines and causes the transformation. That blood, by itself, would instantly stop quantum indeterminacy and kill any earthly thing - except that the nanotech prevents this by reconstructing earth matter into E-matter, while artificially keeping the cells alive during that vital transformation.

3. Gene therapy.

Genes depend on quantum uncertainty to function. Atoms depend on quantum uncertainty to exist. Genes are made of atoms.

Lastly: why would you want any of this? The entire value of a Conversion Bureau story is that humans have to be transformed into Equestrians. That is the main point. Get rid of that and you have no story.

You are trying to work out how to write a Western without cowboys, stage coaches, the 1800's, the Old West, horses, guns, outlaws, sheriffs, or saloons. What is even the point?

If you don't want Bureau stories to exist, too late: they do. People love them. Either embrace the concept or go find another genre to read!