The problem has less to do with saftey concerns from internal problems or outside threat, and more to do with the fact that the plant's mere existence is seen by many to undermine global non-proliferation efforts. From the article:
The US government has spent millions of dollars in recent years helping other nations convert their civilian reactors from using highly enriched uranium to low enriched uranium, a suitable alternative for generating nuclear power that cannot be used to make an atomic bomb. And President Obama is expected to seek further commitments next year from foreign nations to phase out highly enriched uranium from civilian reactors.
But while the Department of Energy set a goal of 2014 to switch the MIT reactor to the lower-grade fuel, that commitment is not likely to be met, according to the Nuclear Regulatory Commission, largely because the MIT facility needs a special kind of new fuel to maintain its uniquely high density core - fuel that will take years to develop and certify before it can be manufactured in sufficient quantities.