Judging from the information I've seen and read about him, he seems to have been killed for the reasons cited in the email Rerevisionist received from Peter Eyre - Middle East Consultant:
It became apparent that the white government of the RSA did not want these nukes to fall under the control of a black government and arranged with the US to have all 9 sent to the US for decommissioning.......however the UK government asked if they could purchase three as standby weapons to use on Saddam in Iraq.
The three were illegally purchased using tax payers money but channeled via the private sector and involved many high ranking political figures........of this money 17.8 million pounds was siphoned off and ended up in the Conservative Party Election Fund.......they were shipped to Oman without security and were stored without security in a private compound and were then stolen by the same arms dealer that sold them.
Dr Kelly was responsible for the safety and inspection of the weapons prior to the release of the funds and this is one of the main reasons why this poor man got assassinated.
The above quote appears to make sense if Dr Kelly believed in the existence of nuclear bombs. But it also made me wonder for the first time if there was the slightest possibility that he may have threatened to expose the non-existence of nuclear bombs - unlikely, I know - but possible.
Even if he had exposed such a colossal lie, would anyone have believed him (besides us)? Probably not, so that would not likely have been enough of a reason to execute him.