为什么选D

强调句，从句只能用that替代主句表语成分中被强调的成分。
句子原本的形态是The drug,not the disease,killed him two years ago.
强调的不同，语境不一样，意思也有差别。但是从句被强调的部分只能用that替代。给你做其它部分被强调的变换你参考下。
1....it was him that the drug, not the disease, killed two years ago.
2....it was two years ago that the drug, not the disease killed him.

PS：not the disease在语法成分中做状语成分，不是关键的语法成分。所以在分析句子语法成分时可以暂时剔除，就很明显可以看出这是个强调句式了。

D....that
因为 that 已可代表前面所说的 drug

that 定语从句，that 在定语从句中做主语，而not the disease可以认为是插入语，先行词和从句被分开时有that引导定语从句。不能用which

A which

D 这个句子是典型的腔调句。The medical record shows 是干扰因素，与本题答案无关，后面的it was the drug,not the disease,that killed him two years ago.是标准的腔调句It is .......that .....格式，这种句子中，只用that, who 两个中的一个，没有其他的表达。该题很明显“The drug" 只能用That，如果换作是某人，那么可以是”Who

逗号是因为有插入语,并不是非限制性定语从句
本句属于强调句,强调句的句型就是it was ...that...
另外,识别是否是强调句就是看 it was拿掉句子是否成立,如果成立就是强调句了