Thoughts in order of thunking:
1) I would not breed a runt. Runting is generally caused by some sort of genetic or congenital defect. I would eat her.
2) Runting is not likely to be passed on but if it is a genetic flaw then the genetic flaw has a good chance of showing up in the offspring or grand offspring. This is not a sure way to produce small pigs. It is important to understand the difference between true runt vs just progressively smaller animals. She might be either.
3) If bred to a normal boar she will likely throw normal size piglets which may be very hard on her. Thus go with a small breed if you can.
4) If you're dead set on breeding her then get the best genetics from a small breed into her that you can which will tend the offspring towards smaller and hopefully cover up any genetic defect if she has one. Might work. The easiest, safest way to get the best genetics is probably AI unless you have a
local boar. I'm very cautious about Rent-a-Boar for biosecurity reasons but then I've got a lot more pigs to protect. Doing AI gives you a chance to practice AI which could be valuable. This avoids PEDv, hopefully, as long as it can't be transmitted in semen and isn't in the source boar. (Ick.) On the other thought of PEDv is that you'll be exposing her which then protects the piglets according to my understanding of this disease.
But I would eat her.