I am remembering that conversation a little differently. I thought that Dogen was telling Jack what the consequences would be if Sayid didn't take the poison: that the "darkness" infection would grow until it took over completely--as it did with Claire. In other words, because Claire didn't get the "cure", she went nuts.I might be wrong but when Jack and the Japanese guy . Dogen ?. When they were having a conversation Jack asks him how he knows the pill cures the "infection". Dogen's response was "because you're sister had it". Now I may have heard it wrong and he actually said "your sister HAS it".
If this is the case the poison pill doesn't kill the body. Thats obvious because later on Claire is seen shooting the two others.