As far as I know Martin said that with one of the fan theories they actually find out the end of the story already, and that Howland Reed will show up in the end. So I don't think their child was stillborn.
I really hope that Howland will have much more to say about it than they are just Jon's parents. I believe he has a right, acceptable explanation about them, even if Lyanna went with him willingly. But if not, don't forget that Lyanna was only 16 when died, maybe 15 when everything started. This is the age when people are the most selfish, when they think the world is around them and they can do whatever they want. Robb was 15-16 too, when he decided to wed Jeyne Westerling, doesn't caring about the agreement with the Freys. Both he and Lyanna got their "gift" for it.
Anyway when it comes to pairings, people usually likes the contrary. They like Sansa and Sandor because they are the beauty and the beast. They like Jaime and Brienne, beauty and the beast again. They like Jon and Ygrette, who are a man of the watch and a wildling, even with a totally different personality. I think this is what makes that much people like this particular pairing as well. While one of them is the ice, the other one is the fire.