To “rebut” an argument is to offer a counter-argument.
To “refute” an argument is to disprove it.
So the CNN headline-writer who wrote the headine:
Blackwater chief refutes “negative and baseless allegations”
was in error.
This has been another message from your friendly local Language Police.
Update The CNN headline now reads “disputes” rather than “refutes,” though it’s still “refutes” when you do a Google search. Good to know that the LP has moles in some of the big news organizations.