I also changed form an LT to a GT because of the reduced weight. The extra power sure didn't hurt, either.
And I've ridden through London, so I know exactly what you mean.
You have several choices here. One is using just a top box for commuting. BMW makes a large 49L box, and a smaller 28L box. Both are well made and spacious, pop easily onto or off of the factory rack, and can be keyed to match the bike. The downside is that they only come in silver (some guys have them painted to match), and they are typically BMW pricey. But either case is the simplest, most elegant solution.
Another choice is to go with an aftermarket case like a Givi. They make an adapter plate for the GT/RT (same basic rear rack), but even with the adapter plate, they're still cheaper than the BMW stuff. And they come in several different sizes as well.
Or you could leave the saddlebags on and get some City Lids. These are replacement saddlebag lids that are thinner than the factory lids. You won't be able to fit a full face helmet in your bags, but they will reduce your rear width dramatically. You can see the lids in this thread
, this thread
, and this thread
. They are available from importers in France
and the Netherlands
. The Netherlands link also shows the silver BMW 49L top case. Note that the saddlebags and trunks for the GT and R12RT are exactly the same (except for body color), so sometimes these parts are listed under the R12RT.
As for mirrors, you can get the oval mirrors off an old-style 2002 K1200RS that will fit into the mirror mount holes in your existing handlebar controls. Then you could remove the fairing-mount mirrors and get the bike down even skinnier . . .
But what I've done is to change none of that at all. The factory mirrors are a good judge of the bike's width, and are actually already wider than the saddlebags (measure it out - it's true even if it doesn't look like it). And the saddlebags are down low, so if you your mirrors clear the gap to the car/truck mirrors, then your bags will easily clear their bumpers.
Hope that helps.