Coulson knows that May will never understand why he had to tell Skye the truth, she will try, he knows she will, but she is simply not wired that way. She is wired more for deception and lies because that's how you keep your cover and stay not-dead.
Why bother telling the truth if it can get you killed? There was no need to tell Skye the truth and now that she knew it, all it had done was put her into more danger. There were people looking for her and all they had done was tell her (and knowing that Sky had no self-preservation skills and would probably announce it to everyone onion the hundred mile radius).
But Phil knew it had done something more.
It had given Skye a family to belong to, the chance to know where she'd come front even if the news wasn't good, and Skye was being such an optimist about this that it made his heart hurt.
There was something just that little bit more confident about her smile.
There is a surety in her eyes that this is where she belongs.
And no one can take that away from her.