Hi. You have to be really careful about how you use a disconnect switch to the battery. If you throw the disconnect to the battery to kill the engine (i.e., you break the connection while the engine is running), you are apt to fry your alternator's diodes.
Car's don't usually have battery disconnect switches, but most powerboats do have one, and as a boater and certified boating instructor (U.S. Power Squadron and U.S. Coast Guard Auxiliary), I can say with authority that it's not uncommon for someone on board to mistakenly throw that switch (the same sort of device you're considering), and fry the alternator.

In the old days of generators (really old days :-), you could disconnect the battery while the engine is running and expect it to keep on going without harm, but not with an alternator. The battery is a "moderator" that keeps voltages in control (and with feedback to the field) -- remove this, and the alternator can spike the voltage up to well beyond what is safe for electronic components. Like I said, "toast"!

re: "...just using SW1 to switch the main current will not kill the engine as well, because the alternator just keeps on feeding the grid, but will this work?..."
Such a switch is a good idea, if you're going to disconnect the battery after the engine is shut down, to protect the battery from unnecessary drain (the sole good reason for you to use the switch), but with all your commentary about "killing the engine", I'm afraid that you're thinking about using this as an emergency shut-off, or something like that. Don't!

re: "...but with 2 or 4 little contacts in the base for switching the alternator output as well (call it SW2)...."
I would be very careful before relying on this scheme to protect the alternator -- if that's what you're thinking of -- because if "SW2" doesn't disconnect the field within microseconds of disconnecting the main battery connection, "SW1", your diodes may be toasted.

If you need to have a quick disconnect, there is a device sold in serious boating shops and catalogs that is designed expressly to allow one to disconnect the battery (as you want to do) without damaging the alternator. It's designed to prevent such damage (because it happens so often among boaters, as I told you above). Look into this (ask for a device to protect the alternator should someone throw the battery disconnect -- the boat shop owner will know what you want).

Good luck. And Happy New Years.