You can't seriously say that games don't regularly get that level of content cuts. Most of the time it ends up being shit that easily gets spotted as "This is a sequel thing then" or "it's gonna be dlc".
Remember Liara's questline being cut from ME2, along with two whole squadmates? Fast forward to ME3 and we ended up getting severe cuts that people were able to identify because of the leaked script from the beta. And then there was the total dlc plan redesign as a result of the backlash that was rumored to originally involve a cerberus "phoenix project", a collector ship that was away from the core during the suicide mission of that game, and a more involved dlc to expand the endgame, as paid dlc. (much of this ended up getting confirmed via the multiplayer dlc that came later, as it wasn't effected by the restructuring, and still matched up with the expected timelines of those original leaks.)
The uncertainty of the future of the series is what makes this a more hot button issue. In ANY other climate it would have just been seen as "Oh they're gonna have the next game open up with the liquid thing."
Think about MGS2. That game doesn't resolve vamp's fate, it cut out gameplay segments from the opening (an unwinnable fight against ray, running from the flooding tanker), it cut two bosses (old boy and chinaman), most of the ending was cut as a response to 9/11 (which is actually what gives the game as much of a dreamy weird feeling at the end that fueled "is it real or a vr?" more than was intended, snake vs ocelot at the end was also cut, and a major water segment between big shell and arsenal gear was also cut....there were gonna be sharks in the game!), and then the game doesnt even wrap up it's own loose ends with the patriots plotline or anything. But it was fine because they were gonna wrap it all up in MGS3, right? At least they found a way to bring old boy back as the end. (This is just what happens) You wanna know some serious gameplay cuts? Hey MGS4 had 3 entire characters cut form the game. Two of which were probably going to be bosses!
http://metalgear.wikia.com/wiki/Adam_(cut_character)
http://metalgear.wikia.com/wiki/Snake-Man
http://metalgear.wikia.com/wiki/Johnny_(Soviet_soldier)
What it ACTUALLY comes down to is how capable you think a future game can be without kojima, and further down this konami rabbit hole. Eli's mission being cut, if we didn't know so much of the behind the scenes drama, would just seem like a sequel stinger "if ever there was one." The problem is people were looking for closure to the series with this one. (The irony is that we already got closure back in 2008 with MGS4.)