It was trying to use his memories of Yemi to guilt him into working for MIB's agenda. Eko manned up and said he had nothing to be sorry for, which may be true, since we don't really see him actually doing anything bad aside from some relatively morally-nuetral smuggling. The only violence we see him commit as an adult is more or less justified.
But Eko's declaration that he had nothing to be sorry for (and certainly nothing for which he had to answer to a smoke monster on a mysterious island) meant he was a potential problem for the monster. At the least, he would not be a useful tool, and thus could be discarded.