He may have been doing this country a service by trying to minimize the impact of Clinton on the military.
High-ranking generals are often confronted with a "damned if you do, damned if you don't" situation when dealing with a corrupt President.
For example, Dereliction of Duty, by H.R. McMaster, explores the relationship between the JCS and the Johnson administration at the outset of the Viet Nam war.
McMaster finds that the generals were in the position of a.) resigning, so as to register their distaste for the orders they were being asked to carry out, and thus have no influence over events or b.) hanging in there and trying to influence events as best they could.
I tried putting myself in their place and concluded there was no good answer.