you are a runner

Not recently. I'm hoping to avoid a knee replacement.

your mother, who certainly knows

She does, for the record. She was a blue-ribbon barrel racer for years.

Are the animals themselves better off for having been engineered for racing?

Ah, now that's a different question. Whether we ought breed selectively, and whether existing animals ought be used (or allowed) for a purpose are different.

Don't they break legs all the time?

The Fatal Injury Rate in the US is %0.192 or about 2/1000, and has been around that rate for the last twenty years.

You and I are not the products of a series of forced marriages, selected for running skill

I think this question is also two different issues. Whether selecting for skill, in humans or animals, and forcing such, are different. The biggest moral problem with eugenics is forcing breeding, and murdering bad specimens. If two Olympic runners voluntarily had a child for purely genetic reasons, would that be bad? What if a thousand did it?

But horses can't make decisions. So, we come to a third issue: do we have the right to impose artificial selection on animals? I don't think that's significantly different than any other animal rights question.

people should be forced

People, no. Animals? Once again, animals can't legally make decisions. Although, if a horse is greatly opposed to doing something, no amount of whipping will force it. And excessive whipping is abuse, and illegal in the US.

It's hard to say how much better.

Also hard to say what is better. Is it better to live in comfort, or to push your limits? Each human has to make that decision for themself. Unfortunately, horses can't.

If a horse were to express a preference to do something other than run fast, what happens?

No simple answer. If it expresses strongly enough, it becomes a pet instead of a racehorse. Or maybe it's illegally abused. Depends on the horse and owner.

Whipping

Yes, I'd probably support stricter laws on that. That said, the riding crop is a slap, not a punch. Yeah, slapping people is bad, but punching people is exponentially worse. You don't go to jail for slapping someone, and you shouldn't.

Horses seem beautiful and intelligent creatures

In my opinion, having grown up on a farm, the cultural perception of horse intelligence is a projection of our appreciation for their beauty. In my opinion, a horse is about as smart as a cow, and measurably dumber than a pygmy goat.

capable of expressing preferences

But yes, even a hamster is capable of expressing preferences and experiencing suffering.

In summary, I think most of your concerns seem specific, but actually reduce to animal rights. Which don't have a simple answer (unless you're an extremist). Animal rights are complex for the same reason child and invalid rights are: because they're not legally capable of making decisions. Any time you (or the state) have to make a decision for something intelligent, it's difficult, because everyone involved believes the creature wants or needs something different, often fiercely.