I believe you are wrong on him offering advice. That would be the job of the joint chiefs. His role would be to implement the decisions coming out of White House and Pentagon. Might he be consulted? Could have but I dont see any evidence that he was or that the actions taken where his recommended actions.
Well, I consider notifying the Yemeni government that the Cole would be docking at his orders, complete with refueliing with inappropriate security, followed by RECOMMENDING that no retaliation be taken because of atangonizing the Pakistanis, damning enough evidence.