Could you post a picture? The "problem" is that disc surfaces are completely exposed to the atmosphere so will rust. The surfaces swept by the pad friction faces are the important bits. within reason rust on surfaces not swept by the pad are irrelevant - as long as not corroded to serious excess which would weaken the disc structure.
In everyday use the exposed surface of the disc rotor where the pads rub will probably show some evidence of light rusting after a night standing out in the rain. Here's a picture of a front disc on my Ibiza after standing for just over one day out in the rain on the hard standing outside my garage:
and here's one of a rear disc:
You can see the very light rusty spots on the face of the disc but this will be removed by the pads after the first or second application of the brakes as you drive away, thus leaving a bright shiny surface. You can also see the much more heavily rusted, narrow band on the outside and inside of the face of the disc where the pads don't rub. This is absolutely normal after some time in use. In fact these discs and pads have now done nearly 28,000 miles and are still in excellent order easily producing an MOT pass figure and attracting no advisories.
By way of contrast here's the discs from my older boy's Punto:
The first picture shows the "front" of the disc, by which I mean the surface you will see if you look through the wheel (nice and easy with many modern alloy wheel designs) However, don't be fooled into letting this fool you into thinking all is well. The second picture is the rear face of the same disc. You'll have to get right under the car or take the wheel off to get a good view of this. You'll notice it's not in anything like as good condition as the more easily checked front face. Not only is it's surface quite deeply scoured but around the outside there is deep and crusty rust which will simply be ploughing pad material off the face of the pad so not allowing it to grip the disc. It'll only be providing stopping power where it's gripping on the smoother polished surface. This is not at all unusual in my experience so don't think you can accurately assess the condition of your brakes by simply looking through the wheel at the front side of the disc! Under these conditions you'll find the pad in contact with the rear side of the disc will wear more quickly too so you can't even accurately assess future pad life from what the outside pad is looking like!
The Fiat brakes had been on the car for about 5 years and in fact still had a reasonable depth of friction material on them:
The car drove well and braked smoothly without pulling to one side at all. I've no doubt that it would have produced a braking performance which would have passed the test but after another year? I wouldn't be so confident. I like brakes on "the family fleet" to be as perfect as possible and Punto brake parts aren't expensive so the decision to renew was not difficult. I think a diligent tester would probably stick an advisory on the old discs if he/she looked closely enough. If you feel tempted to just stick a new set of pads in when discs look like this then i would advise against it. Not only will it take quite a number of miles for the pads to bed in - That is wear to the ridged shape of the old disc, and performance will be poor while they are doing this - but the pads will wear quite a bit more quickly too. Just not worth it. If the disc isn't A1 just do discs and pads together.
As Mike mentions above, these rust problems are worse in areas where lots of salt is used on the roads - and that's us! I like to go round the edges of my discs every year at service time with either a medium grade grinding disc or chipping hammer and get rid of the worst of the crusty rust. If you let it build up to excess it can often make rubbing/grinding noises and these can sound quite alarming although mostly it's a harmless noise.
Used to be that you could run through a couple of sets of pads to every disc in the old "asbestos pad" days. Now it's not unusual to be doing new discs every time you renew a set of pads. Oh, and of course, don't even think of doing just one side will you?
