I think what irks me is that for Otis to have done it all alone, suddenly the zombies aren't dangerous. Whatever way Otis could have got them into the barn, it would surely have been safer to have the other farmers actually help him with the ordeal.
Equally it's a bit difficult to believe that nobody saw him do it. We've had so many scenes where Rick's or Herschel's group have seen people walking or riding out of the treeline and crossing the fields to get to the farm (and even the barn) that it seems a bit odd that nobody saw Otis leading a girl zombie to the barn.
And if nobody did see Otis doing this, then they've been remarkably lucky during the zombie apocalypse, as Otis could quite easily have been a pack of zombies making their way to the noisy, lit-up farm. I know Herschel gang aren't pictured as being the savvy survivors of rick's group who always have a lookout, but even so...
As for why Herschel, or the others, didn't speak of it? It seems to fit with Herschel's MO: don't talk about it, don't interact with the outside world, keep to yourself, and eventually everything will work out. Herschel kept a pretty tight rope on everything and everyone that was on the farm, and he was very tight-lipped about the inhabitants of the barn - even after he was confronted about it. So I'm not surprised by the reveal.
This is really what I mean by 'why were there no hints to the audience about this?' and it happening in a vacuum.
There's a lot of dramatic potential lost here. Herschel wants Rick's group off the farm. Rick's group won't leave while they're searching for Sophia. Herschel knows that they recently brought in a young girl zombie. Telling Rick's group about it allows them to leave, but also involves spilling the big secret of the barn, which could be a Very Bad Thing.
I think this might have been helped if we'd been shown a conversation between Herschel and one of the farmers. We'd already had a hint of the barn prior to Greg discovering it's secret ("What's the barn for?" "Nothing, stay away from there!") and something equally as vague concerning Sophia ("We've got to tell them about it, Herschel," "No good will come of it if we do. You've seen what they're like") together with some accusatory looks while Herschel is patching up Daryl would have helped.
The Sophia reveal is then preserved, but without feeling as contrived.
I partially agree with Daryl's trail. It's possible that Sophia ended up in the house on the first night, and in the morning got bitten. She could've lost her toy in the river after Rick abandoned her, and it drifted downstream. Part of the problem is that we don't really have much of a clear idea as to the scale of geography the group's been covering. It's that whole vacuum thing coming into play again.
...There's a more terrifying aspect to Sophia's presence in the barn: what if she was found alive and tossed in to feed the family and friends in the barn. ...The supply of chickens will only last so long.
Or climbed in herself while looking for shelter...