Media Matters is a useful website, especially when it examines the assumptions behind many a false cable news report, but it would do a much better job if it got it's tongue out of the anus of the Democratic Party. A female Presidential candidate rhetorically asking how she is equipped to deal with "evil men," and alluding to the husband who was brutally disparaged by his foes while he was President, and who, on numerous occasions, betrayed their wedding vows, but whom she still loves, is being witty; it's taking a potential weakness (her marriage-of-convenience to Bill Clinton) that's on the subconscious of everyone in the audience, and making a self-deprecating reference that lightens the tension.
On the other hand, perceived references to "Ken Starr", "Newt Gingrich", "Dick Cheney", et al., aren't witty; they're banal partisan jibes. Regardless of what Hillary Clinton intended, the joke is only funny (and she did say she was trying to joke) if the "evil men" line refers to her husband. The Democrats already pay people whose sole responsibility it is to generate propaganda for the party, so unless Media Matters is getting a healthy stipend, it isn't worth it to be compromising it's integrity on something so silly.