Despite the “realism” the author tries to invoke, that’s not how applied research with genomics work. An adult human body has more cells than stars has the Milky Way, and trying to splice the DNA into them all would be impossible.
 
This is how it really works: You write a preliminary hypothesis to get some MONEY to start with. You test the bee’s proteome against the mutagen, you identify the Hits, then the Leads, which are the active principle and elaborate another hypothesis that you present to your superiors for MORE MONEY, design a plasmid (Or BAC, or whatever if the gene is too big) that holds the gene of interest, insert it into E.Coli or CHO cells and let it produce the protein. Then you tamper with the inserted genes to look for the most efficient variant. You test it on tissues. Then you ask for even more money and start preclinical tests on mice, rats, dogs, pigs and primates (or horses, in their case). Then you ask for more money yet again and try the 4 clinical phases.  
It would take 15-30 years, most likely.
 
Zecora would have saplings by then. Magic is better and more fun.

That’s intresting

@Ajedi32  
We’re already dealing with a disease that turns animals into plants. This is definitely outside the realm of conventional, nonmagical biology.

All those posters about lab safety, and the girls didn’t even tie their manes back. They’re getting foreign DNA everywhere, and Fluttershy’s mane is practically guaranteed to be set on fire by that microscope focusing the lights.
 
They sure look cute though.

@Ajedi32  
In fairness, bee honey is sort of like bee poop. And everyone knows that poop is the greatest cure of all. As someone who got a C in one of my science classes, Earth Science I believe, I tots know what I’m talking about :)

Shut up Fluttershy, Twilight knows what’s she doing.
 
And besides, we can a lot of profit with a vaccine.

Yeah, the whole “bees are immune, therefore their honey must be the cure” thing was some pretty shaky logic…