My opinion: Not so good, but not so bad either.
You're correct in saying that the magnet debris won't float around too much.Although the case is aluminium, there's plenty of steel in there to stick to. For example - you've probably got a magnetic oil drain plug. Also, the oil filter has a steel case. And even better, there's an internal oil filter which is also made from a magnetic material. I would imagine that most of the debris is already caught. Change your oil and filter very requently for a while (as often as you can afford really, until the oil and magnetic sump plug comes out clean. You can use cheapy mineral oil for these changes, it's not going to be in there long) and you'll probably be OK. But if the bike's being used frequently, take the time to change the oil every other ride or so.
Personally, I'd go a little deeper. While you're changing your oil, when it's drained, take both engine side covers off. You can usually re-use the gaskets if you're careful, but of course, if you don't have spares, you'll need them...
You can check/inspect/clean things a bit better here. There's a kind of oil trap both sides made from the gasket material. Some shrapnel may have made it into these. Also, all the gears you can see, and quite a lot of the clutch are steel. Worth checking/cleaning. (It's not a big job to open the clutch and take a look at all the friction/pressure plates in there) Also peer behind the clutch to look at the gear selector mechanism. Bearings are another place the fragments could collect, but unfortunately there's s.f.a you can do to check these without stripping the engine.
I'd also take off the valve covers. Lots more steel here, and some fairly fragile parts, and less oil flow to keep things clean. Inspect/clean the cams, cam chain (turn the engine over several times by hand to inspect the whole length thoroughly) and anything else you can see. You can get a good idea for the general condition of the engine by looking at the cams. If you find significant deposits here, it may be worth considering stripping the engine.
What I'd be most concerned about is a fragment getting stuck in one of the many oil jets and blocking it. Really the only way you can guarantee that won't happen is stripping the engine. It is my personal opinion that this is unlikely (the way the magnets fail makes it unlikely for the right size/shape of fragment to form, let alone make it passed the filters) but the possibility is there. Take a look under the valve covers and you'll have a fair idea about how much made it through.
This is for a 650 (the internals are different on a 1000), but it'll give you a fair idea of what could be involved (worst case)
