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I have an IC (PDIP) I would like to replace with a board and some smd parts. Normal 0.1" headers are too thick to fit in the holes of the desoldered IC pins. Do you know if there exists 0.1" pitch headers with diameter of 0.6mm or less, so that they fit in the holes for the IC pins?

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You can use the machined pin headers. They are available in both male and female versions

Here is the female datasheet that shows the pins diameter, it's 0.51mm
And a male header datasheet , this one shows 0.49mm

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