The key is that it turned out to be a drug that was causing her weakness, rather than (as Buffy originally assumed) a magical attack or incident that removed the Slayer magic but otherwise left her unaffected. The drug may or may not have needed a magical component in order to overcome the Slayer's resistance to poisons, but its primary function was undoubtedly medical, not magical. (Edit: as the OP points out, it was described in the episode as a muscle relaxant.)
Given that, the dosage would have had to be carefully calibrated in any case, in order to avoid leaving her either with too much of her magically enhanced strength on the one hand or leaving her unable to walk on the other. You will note that multiples doses were used, allowing Giles to judge the impact and adjust the dose as necessary.
For the purposes of the Cruciamentum, the dosage chosen was clearly intended to leave her with the strength of the average teenage girl - not the strength of a well-trained athlete and warrior.
As to why the Council didn't use magic to temporarily remove her Slayer powers, leaving her otherwise unaffected, presumably that either isn't possible or the Council lack the necessary knowledge and/or power. (After all, if it was easy to remove a Slayer's power then no Slayer would ever survive long enough to do much good.)