If by "the Administration" you mean the Attorney General or the FBI Director, neither of them can cross the President and still hold their positions. They are both members of the Executive Branch and therefore responsible to him. One thing Mr. Comey might have done is lay out the strong case against Mrs. Clinton as he did--but then, instead of claiming she should not be prosecuted, say he was resigning, because in spite of his conclusion that she should be prosecuted, his superiors had made clear to him they would not follow through on any recommendation to prosecute her he might make. And I strongly suspect that's what he was told.
If Comey had recommended Clinton be prosecuted for violating section 793[f]--which he in effect acknowledged she did--nothing was to prevent Justice Dept. prosecutors, at the direction of Ms. Lynch, from fixing the thing anyway. One way they might have done that was to convene a grand jury to provide the illusion they were taking action, but then present that grand jury only such incomplete and diluted evidence of her guilt, and do it as if they were defending her instead of prosecuting her, as to guarantee she would be no-billed. And Comey would have been made to look like a relatively minor official who had tried on his own, by misusing the law, to determine the outcome of a presidential election.