I can't answer about using hot swap with the Z68 intel ports as I haven't tried that.
But the Marvel eSata ports *DO* support hot swap. I'm using them with eSata devices. There is a driver properties page (Computer Management, Storage Controllers, Marvell 91xx SATA, Policies tab) where you can set "Enable safely remove disk". That will allow you to shutdown/remove the eSata devices using the standard windows "Safely Remove Hardware" functionality.
Make sure you have the latest Marvel 91xx driver, as the earlier ones didn't support hot swap. The one currently available with other DZ68BC downloads will give you version 184.108.40.2066, which supports hot swap.
Let me know how it goes, I'm interested in your experience good/bad. I don't fully "trust" the Marvell controllers, as I have read a lot of complaints about them. But so far (knock on wood) they have worked perfectly for me -- although admittedly all I am using them for is eSATA with portable drives.