Attempting to answer the OP's questions:
Yes, I've coached women with similar problems. It can be frustrating, but you've done well to have identified her condition. A relatively high number of females get this–particularly vegetarians. (Actually, I've never coached a strict-vegetarian female who *didn't* eventually get problems with anemia. Lack of B12 and dearth of assimilable iron, I guess.) You're right: variable performance is a hallmark of this condition (and also of eating disorders). However, now that she's been diagnosed and is being treated, you can look for more of a steady progression. So the question is, what should her training be like?
In her present condition, she's somewhat like a person running at altitude. Easy-paced continuous running should be possible, but if the pace has to slow down so much that her mechanics change to a "jogging" mode, then she's not going to benefit much from that. If you send her out for a distance run, tell her to take a walking break whenever her pace starts to bog down–or, even better, coach her to take those breaks *before* her pace bogs down! You definitely want her to feel like the aerobic work is building her up, not exhausting her. You might experiment with substituting a bike ride or swimming or rowing or elliptical or other aerobic machine for the pure-aerobic work–the idea is that she should always associate aerobic *running* with freshness, not exhaustion.
Just doing easy running will not prepare her for races, of course; but short-rest reps are really tough for the "altitude" runner, because she can't neutralize the lactate buildup very well. And in general these anemic kids respond badly to large (total) loads of lactic acid/anaerobic work. So if she's doing quality work, either have her take longer rests between reps (maybe doing every other rep with the rest of the kids); or just go with a single good-quality effort, perhaps 1000 or 1200m. Strides and sprints are generally fine, actually, provided that they're short enough and followed by enough rest to be mostly alactic.
Patience (especially with race results) is called for; so if you can show her some kind of steady progression in her *training*, as her treatment improves her anemic condition, that should help to keep her (and you) motivated. Good luck to you both.