As for whether there's really a "superior," input method, not really. K&M does allow for extra precision and can yield startling results of accuracy and speed if you've got a lot of experience and a high DPI mouse. Analog sticks can't and don't provide the same degree of precision- hence, aim-assist. If it weren't for aim-assist, next to nobody would be capable of effectively using a controller in an FPS game, and *certainly* not in a competitive way.
Folks who are used to one of the input types typically resent the other. Few people are "ambidextrous," and can honestly say they're not better acquainted or preferring of one over the other. Assuming no mod skullduggary is going on, an experienced K&M player should be able to snag pretty good accuracy and so should an experienced controller user (aim-assist is carefully designed not to be *too* forgiving, just to make it so precision work with an analog stick isn't impossible).
Infinite should follow MCC's lead and let people filter input preference as a selection criteria for Matchmaking, but I don't think it'll be a problem for the game to support both input types. Of course if you're having a bad match and are playing against different input players, you're going to tend to blame your losing on their method receiving preferential treatment (just like people have blamed lag since the dawn of online gaming).
TL;DR: K&M makes precision shooting a matter of clicking *exactly* where you want to hit, which is a breeze for experienced PC gamers but can be difficult for others. Aim assist exists to compensate for an inherently less precise input method in controllers, but isn't enough to make a player who isn't experienced with a controller "good". Leaving the option to filter out input types to match yours is a good idea for 343i to carry forward into Infinite, but I do think the option to use either should carry on too.