You are just wrong. Ford pardoned Nixon before any formal charges had been filed. Carter pardoned the draft dodgers before any charges had been filed. How would Obama pardoning Clinton be any different?
I'm sorry, but your both of your premises are incorrect and easily disproved.
(1) Regarding Nixon, Gerald Ford had been in office for a month, and the basis for charges leading to prosecution were before Ford. He had only two alternatives from which to choose: (a) lay the charges; or (b) pardon Nixon as co-conspirator. The other members of the conspiracy were not pardoned, nor did Nixon while President pardon them.
A month after taking office, President Gerald Ford addressed the nation on television to announce that he had decided to pardon Richard Nixon. You need to read Ford's text of the pardon (click here). Here is an excerpt from the article:
"Now, therefore, I, Gerald R. Ford, President of the United States, pursuant to the pardon power conferred upon me by Article II, Section 2, of the Constitution, have granted and by these presents do grant a full, free, and absolute pardon unto Richard Nixon for all offenses against the United States which he, Richard Nixon, has committed or may have committed or taken part in during the period from July (January) 20, 1969 through August 9, 1974."
Note that the pardon only extends to acts performed against the United States, and included the period only of his holding the Office of the President; not, say, his dry cleaner's bill or foreclosure on his mortgaged property, or of offenses committed before or after his Presidency.
(2) On the second point in which you erred, Jimmy Carter's pardon of certain (not all) draft evaders was extended only to those who were: (a) citizens not already sworn in; (b)standing convicted of non-compliance to the Military Service Selective Act; (c) the act of evasion did not involve force or violence on the part of the perpetrator; and (d) the pardon was by application and approval for it, not a general one not requiring an actual individual remission.
Please read the instructions for applying for the pardon (click here).
The pardon was already formulated and ready for signing, but only on the day after Carter stepped into the office of Chef Magistrate.
Clearly, from the Nixon-Watergate example, Obama can not make a pardon stick for when he was complicit for Clinton's misuse of the Cabinet position.
Let me add that I really hate it when I have to take the time and effort to do your research work for you.