Obviously, examples where a player got injured are extreme and obvious exceptions to the rule (ie Nishikori vs. Nadal in Madrid), so I wouldn't focus on that.
I'm with you though, that it is too simplistic and not that cut and dry in general. I think the margins in tennis are so small (literally dictated by inches) that being so dogmatic isn't wise. I mean, what if Fed's first serve on match point doesn't clip the top of the net? Half an inch up and he probably ends up being "the better player."
That said: "Clearly, Roger played better although Novak ended up winning."
There is more to tennis than how well you strike the ball, which tactics you employ, etc.... Playing better and being the better player aren't necessarily 100% the same although they're close. In other words, Roger played better, for the majority of the match, I don't think that's debated. But does that make him the better player on the day when Novak played the big moments/big points so much better?