ECU with 2 maps.

In short, yes
With megasquirt, you can have table switching - on a switch!
So you have 2 fuel and 2 ignition tables. Flick a switch, and it goes from set 1 to set 2.
Easy in theory, in practice - a bit of a pain.

The easiest option is just to map it properly in the first place. If the maps are good, then you'll have both power and economy in 1 set of tables, with no danger of melting anything if you have the wrong set selected .
See the way the tables work is pretty clever if your using speed density method - the modes of operation of the engine are pretty clearly defined, so there is a 'power' area, a 'cruise' area, an 'idle' area etc, and they should all be optimised in a good map, without affecting each other.

Megasquirt allows you to control anything by defining 1 or a pair of rules, so in theory you could hook your supercharger pully to come on when your throttle is 90% closed AND your engine is at least 60 degrees C for example.
It's just a low-level logic output coming from the board which you can control anything with, by adding a booster circuit. Exactly what sort you need depends on what sort of device you're trying to switch.

If you don't mind flicking a switch when you want more power, you can make a manual override for the megasquirt controlling the charger. If the measuring and mapping is properly done, the megasquirt will be able to adjust to charger/no charger and you will get the economy you want.

this can all be done with megasquirt.... but you would question the point of it really - I was going to run an eaton m90 on a mag clutch with table switching for my original 2.5l engine but that was purely because it would be show-y and a unique challenge.

The trouble is in building the boosted engine to get high power from the supercharger you end up with a much less efficient engine when the charger is off, this coupled with the fact that you need an intake that bypasses the charger (probably a far less efficient route than on most standard NA inlet tracts) means that the actual economy you gain is smaller than you'd hope.

If you want an engine that is "economical" (evidently you don't want economy too much or you'd have a diesel) and nice to drive then the best bet is to build the engine (supercharged or not) to your power expectations and then map it very well. As mentioned above, a good speed density map will be economical for cruise and high power for foot down times.

if you only want the charger to come in at a certain rpm/load, then you don't need a switchable map at all...just need to properly set up 1 map so that when cruising (light throttle loads) the charger is off, then above a set throttle position you have the charger kit in and the fuel/ignition tables adjusted accordingly ;D

Was thinking about doing the same with the williams ECU as I've got a fuel saver map which doesn't always play ball. Worked out I could switch it physically or even use a 256bit eprom rather than 128bit to switch internally. Lot of work though. Just learned to tweak the car so it runs properly on the one chip. Still getting there.

nitrous or even a nitrous assisted turbo might be better then trying to re-create mad max, clutch engaged superchargers don't work for proper engines (read V8's) getting one to work on a small engine hardly seems worth it, and its not like it'll be pokeing through the bonnet for all to see,

saw a twin turbo'd 3.5 ltr v8 in a moggy once, quickness/loudness is controlled by the right foot

Surely turbo applications could benefit? i.e. if you wanted to be able to run switchable boost, also run 2 (or more) fuel maps, and drive boost control from these maps - i.e. map A 15 PSI of boost and not much fuel, map B 25 PSI boost and more fuel?

Naah dude, that's what I call a complicated mess.
I think if you wanted to have different boost levels on a switch, you'd use a boost controller with that functionality, and have the tables mapped safe to the highest boost that your machine can take.

Typical scenario:
In positive manifold pressure your maps are slightly to the safe side of 'just right'. How big the margin of safety is down to your and your mappers confidence in the engine. Your mapper will know from their experience and tools at their disposal how much is too much .
Fuel wise - leaner than this gives more power, but nears self-meltdown.
Spark wise, more advanced than this will give you a bit more power and will start to knock and det, leading to bent rods, blown headgaskets and pitted pistons/chambers.

In the same way, in vacuum when would you need 2 separate fuel/ignition tables, when the 'right' set will offer you the best power and economy . Leaner than this will make your engine and EGT's hotter. More advanced is same as in boost you'll be reaching knock threshold and probably det, blowing your gasket.

KISS = Keep It Simple and Sideways ;D not be thinking about what mode you're in all the time.