As you know, I thoroughly hate the ncaa, mainly for their inability to manage, and even manage in an ethical manner. In all fairness though, this analogy is a bit of a stretch.
First, from my understanding, the lead investigator was looking at the DV. If true, then that still ignores the reports that EE didn't cooperate with the league. I think, by and large, the innocence of EE in the DV has been established (and talked about by IE on a thread), but a lot of the harshness of his suspension stems from him being reluctant to, or altogether not, cooperate. So my point is if somebody investigating him for DV finds him to be "innocent," that still doesn't necessarily explain that he might have been a total POS in the entire process, and thus still worthy of a suspension.
Second, the ncaa and nfl are two entirely different animals. The league is, more or less, an association of 32 businessmen (and woman) looking to run a business and make money. The ncaa is an association of several hundred schools (who are mostly run by state employees, by way of federal mandates) who claim to look out for the best interest of amateur athletes, by making themselves billions of dollars in the meantime. These are obviously 2 oversimplifications of the 2 entities. I mean in your example, yeah, I'd be pissed about BW and the ncaa, but I think BW and EE are kind of an apples and oranges comparison.
The nfl catches a lot of heat, publicly, because 1)It's by far the most popular sport we have in the U.S. 2) People get pissed off about the league's tax-exempt status (even though they pay a shitload of taxes, but done so on a basis of, and through, the 32 individual teams. 3) People think they operate with a genuine government exemption. Which is kinda BS because they (and literally only a few other entities) are truly monopolies...but still aren't really. 4) Patriots fans (which is probably the loudest and most vocal dissenters of RG and the league office now, and for the past 10 years).
I'm not really sure suspending EE is another legitimate reason for the league to catch a ton of flack.