These took only a few hundred to a few thousand generations:
A LOT of morphological change happens by a few mutations. Consider how much dogs have changed from their ancestors, with a small handful of mutations.
Plasmodium falciparum has a genome size of ~23 megabases and a mutation rate of ~1 - 10 × 10-9, which means you find a mutation in roughly 1 out of every 40, to 1 in every 400 individuals.
Mammals typically suffer dozens to hundreds of mutations pr. individual pr generation. Many of them are rather large-scale rearrangements or insertions due to transposons.
You simply cannot compare plasmodium falciparum to mammals in that way, and you can’t extrapolate the rarity of “solutions” to chloroquine resistance to the “rarity” of mutations that produce morphological change.
These extrapolations from chloroquine resistance you ID guys like doing are ridiculous. They don’t work. The math doesn’t work.
All adaptations are not the same. Some really are accessible from inordinate amounts of positions in sequence space (increasing the amount of hormone expressed for example, can have effects of many parts on the body simultaneously). And there are many more ways of increasing the amount of some hormone (duplications can increase dosage, better binding by transcription initiators can increase the dosage, reducing function in repressors can increase the dosage, etc. etc.), and several different hormones can have similar effects.
In this way many more loci can contribute to changing body morphology and are therefore way more accessible to evolution, while a particular transporter interacts with a particular drug perhaps only through a few specific residues that epistatically interact.
You REALLY need to stop falling for this silly appeal to chloroquine resistance that people like Behe and Bechly keep doing when trying to undermine macroevolution. They just aren’t the same thing. They don’t work in the same way.