If they can replace the stupid drama of "will they or won't they" with the much better and more interesting drama of "will Chuck remain his charming self or be corrupted and bad and evil by the spy biz," then Chuck and Sarah could have sex and guess what, the sky won't fall! Here's how it could work:
Chuck had that little problem with The Pill, even tho Sarah warned him about it. (Those who aren't up to speed, that isn't as strange as it sounds.

)
Chuck and Sarah finally decide to have a real romance. But the snake in the grass is: Chuck knows he can never be A Real Spy without the dratted pill, which will turn him...
EVIL! Just in time for the season cliffhanger.
Next season, Sarah and a reinstated Casey battle to save Chuck's soul from his newly EVIL! status - he probably joins the Ring and everything - and the series ends with Chuck being returned to Chuckness, running off with Sarah and living happily ever after, having gotten all that ridiculous spy nonsense out of his system.
That really seems to be the only place the story can go at this point that won't just be wheel-spinning.