[Ewww paternal approval ewwwwwww Tony definitely doesn't have issues with his father so his meta violently rejects it. In the meantime, outside of meta, Tony is hilariously ignorant of the vast cast of characters trooping around Skye's memory, in part because he has been completely deceived by them. The lives of spies aren't really his area of expertise, so he doesn't know the complexity of sentiment under Skye saying that. He just says,]

Some spooks just can't stay dead.

[He means SHIELD. As a whole. But you know.]

Who's looking at JARVIS' brain? [he asks.] The hacktivist who exposed the illegal human experimentation behind 30% of the groundwater contamination in Cox Bazar, or Agent Skye? [Yes. He'd read.]