Seems I am a bit late to the party, but it is critical at this stage that you provide us a full list of the lenses you currently have.
For example, you state that low-light photos are not satisfactory. If you do not currently own any fast prime lenses (lenses that can go down to f/1.8 or f/1.4 --- lower numbers are better), then some new lenses will be a better investment. To put things in perspective: Going from a 1000D to a 60D will only give you roughly half a stop of improvement in noise performance at ISO 1600, whereas going from an f/4 to an f/2.8 lens will give you a full stop of improvement in noise performance. Just for comparison, the 6D will give you roughly 2 stops of noise performance at ISO 1600 over the 1000D, but that is a lot of money if you factor in lenses too. In contrast, you can buy a fast prime for roughly R1k new (the 50 mm f/1.8). Other fast lenses will be more expensive, but you can buy many lenses for the R22k that the 6D will set you back.
If you already have fast prime lenses, you could look into buying a flash (speedlight), but not everyone likes flash photography (also depends on your subjects). Keep in mind that you can trigger the flash(es) remotely, so when I say flash photography, I am not talking about the deer-in-the-headlights-compact-camera-flash look. You mentioned macro photography --- adding a remote-triggered flash can do wonders for your macro photos.
Lastly, does she currently own a decent tripod? Could you please provide more info on the type of low-light photos that are not satisfactory, i.e., are they of stationary subjects, or moving subjects?
In my opinion, Canon does not currently offer any crop-sensor (i.e., 700D, 60D, 7D) bodies that are a huge improvement in low-light performance over the 1000D. There are many other good reasons for upgrading to one of those, but Canon has been using the same sensor technology (in crop-sensor bodies) now for about 4 years, which explains why there are not any huge gains in low-light performance going up in the crop-sensor body range. The 6D will give you that instant improvement in low-light performance that you are looking for, but as already mentioned, that is a very expensive option.
Anyhow, if you can provide some answers to my questions above, we can give you some additional options (which lenses, tripods, or flash units) to include in your list of potential upgrades.