I disbanded it as I had not a single scenario where I could deploy it so far, no idea when I finally get to Crete or another naval scenario.
It is a really nice idea to give players a Light Cruiser!

"If you manage to safe the Light Cruiser HMS Insertfancyname, you may keep it under your command for future naval operations. However, we will be focused on desert operations for the near future and you might want to give away the unit for extra prestige."
As nice as it sounds, I think saving the cruiser should just give a little extra prestige and it should not carry over. It is rather going to confuse new players, as it already manages to confuse us. If the Cruiser is to stay, start it as "core" unit and perhaps allow it to be placed by the player, as the sudden inclusion in the core of the player makes it hard to get if this is a core or an aux unit. Regarding those, the campaign doesn't teach new players the differences between aux and core units and the cruiser adds to the confusion.
After Taranto I also had the problem that I started the scenario with a Hurricane, bought another one and next scenario I had only one Hurricane left but still the Cruiser in the core. Another player also reported a "lost" unit that didn't carry over to the next scenario.