Will it work ? Yes. The breaker in the main breaker panel that feeds your sub-panel is the over-current protection for that sub-panel. Changing the MLO panel to a MCB panel shouldn't change the way the sub-panel is wired. Neutrals have to float and the grounds have to be bonded to the enclosure. The main breaker that you're using in the sub-panel now basically becomes a molded case switch (for lack of a better term). Rather than go through all the trouble of changing over the panel why don't you use one of these ahead of the sub-panel instead :
http://www.homedepot.com/p/Eaton-10...uble-Throw-Safety-Switch-DT223URH-N/100151733
If you're intent on using an interlock kit make sure the one you pick is approved for use with the new panel you're installing. The vast majority of the EI's in my area won't accept the ones made by Interlockkit.com or other such manufacturers.