Just as many people idealize Harvard, many others are quick to take shots at it. Regarding its financial status, I have yet to see anything that indicates serious problems. Harvard's endowment got rocked after a period of great returns, but so did a lot of other rich institutions and individuals. The loss of about 30% reflects a pretty aggressive investment position for an endowment or trust, and perhaps Harvard needs to rethink its overall allocation to various investment types and dial down the overall portfolio risk instead of pursuing market-beating goals, but I don't see anything remotely near a financial crisis for the university. The whining about the compensation for portfolio managers at Harvard Management Company (as reflected in one of the posts above) has given way, to some extent, to the recent whining about HMC's investment losses, but there's always a lot of whining from and about Harvard. I was sad to see Mohamed El-Erian leave HMC and replaced by someone who doesn't seem to have his investments credentials, but perhaps a return to stodgy investing (indexing a 60/40 stock-bond portfolio, or something similarly unimaginative) might be a good thing.
As for Harvard's presidency, trading Larry Summers for Drew Gilpin Faust seems like a pretty bad deal. Summers was a hard-nosed leading scholar in an important field who was willing to speak hard truths and take tough and sometimes unpopular actions; Faust is a comfortable old shoe for the faculty of arts and sciences (FAS). But Harvard has survived periods of mediocre management at various other times in its 375 or so years, and it will come through this stretch without any mortal wounds -- to the disappointment of many.
In the meantime, I haven't been taking any calls when the word "Harvard" shows up on my caller I.D.; there are plenty of other people who are willing to shell out tens of millions of dollars to Harvard to get a room on a wing named after them.