Help with a plot point in my story?

[mmllmm]

Okay, so my story is about a young girl in a futuristic society in which her generation is genetically engineered as a part of a government program set out to perfect the gene pool in one sweep because of a threat of war/famine/something along those lines (the boys are strong warriors and women good child bearers/homemakers). The girl is a mishap, a weed- she's tall and lanky and doesn't fit in, and a threat to their program. Her and a boy similar to her are running away, trying to find other people like them, in an attempt to rise up against the gov't.

With that being said, they're running away from being caught because there's obviously some punishment for being different and threatening the gene pool. Should the 'mishaps' be executed? Sterilized? Locked up and used for labor? Put in a separate district/state than everyone else and be forced to live with starvation and poverty? I don't know if there's a line I can't cross, with execution or sterilization, as some recent stories/novels have pushed it pretty far. I guess I'm just curious what your take on this is?
I guess I should've mentioned that the trademark as to show they are different is their fair complexions and lanky bodies. Those who are correctly engineered are dark, shorter, and stocky/muscular.

I suppose they could be branded, or marked, and then they have to live the rest of their life like that and work opportunities are worse, being able to buy things is harder, etc. Good idea... Hmm. Maybe isolation? They're taken to this place, and no one knows about it because the people that go in never come out. They're there for life or something.

[Smithy]

I'd say Sterilizing, and isolation from the normal society (maybe just through a mark on the arm or something, (something showing they are different)), I think that the boy and the girl will find each other in love but not able to express it well before near the ending.
Oh btw, I love your idea

[violet]

Well realistically speaking....if that ever happens, the government would probably take them to do experiments on them to see what went wrong in the first place.

[KhloetheHutt5]

They should be put into the Hunger Games!

[JOSHUA]

have you seen the movie Cloud Atlas? it is really good. based on a book of the same name by david mitchell,. but anyway, my point is that it draws refernce from a movie called Solylent Green, in which people who have died are turned into food for the rest =]
maybe you can make your government program "self sufficient". ie, feed those that die to the rest.

Your main characters could discover this at work, and this could be when they realise the threat to themselves =]

just an idea. good luck!