I don't think any of the founding fathers foresaw presidents using their power to pardon their friends. The whole system is extremely vulnerable to an insider attack - very few tools are in place to work around corrupt leaders.
The US President should have handed this power over to a similarly dusty committee resolving real injustice years ago. This would be less corrupting and more effective because a President is busy whereas the committee would be doing nothing else except investigating the circumstances of potential injustice and choosing how to resolve them (new trial, pardon, etc.)
Interestingly, this pattern repeats itself; countries which became independent from Britain later on often have a far less powerful president, with similar powers to when _they_ left. The president of Ireland, for instance, is non-executive, doesn't have a veto, and can't commute sentences... much like the British monarch when Ireland became independent.
As it stands, it's an anachronism that only survives because it's _really_ difficult to change the US constitution, I suspect.
As for Ms. Holmes, she defrauded very rich and powerful people. I would be surprised if she were shown any leniency at all, never mind a Presidential pardon.