I'm rather interested as to why do you believe that. Sasuke certainly can counter Obito's Kamui in CQC, but how can MS Sasuke completely counter Kamui without Obito simply outlasting him in the end?
Also, didn't read that this is the Obito who fought Minato. EMS Sasuke would beat him with medium difficulty.
The point is analysis. If Sakura and Danzo's guards can analyze Obito's Kamui, then so can Sasuke and faster, in fact. If you remember, going page-by-page history, then Sasuke was the first one to offer an analysis that his attacks phased through. Sasuke can easily use Nagashi in CQC to prevent Obito from Materializing and warping him way. He will have to touch him and if Chidori is running through his arm, I doubt that is possible. Sasuke's reflexes are pretty good as well: Mifune is the master of quick-draw and attack as shown during his battle with Hanzo, and yet, Sasuke was fast enough to completely block his surprise attack, when Hanzo couldn't, despite being engaged in proper combat.
This adds further advantage to Sasuke's case. Once he figures it out that Close-Quarters-Combat can be deadly, then, he'll switch to Susano'o. Itachi basically lit up the whole area by sweeping his gaze around - the initial spawn of Amaterasu followed his line-of-sight. If Sasuke couldn't outrun it, Obito wouldn't either, when Sasuke is the fastest on-foot character in the entire manga, as Minato's best Body-Flicker feat is laughable before Sasuke's, and here, Sasuke was using CM as well with added speed. If the area is lit, then it will help prepare Kirin as well - once that is up, a single blast ends Obito, before he even thinks of reacting. So, he'll end up losing his five minute time-limit, regardless of the fact whether Sasuke knows about it or not.
Then we have the issue of Amaterasu as well. Amaterasu's charge time in MS - not EMS - is remarkably faster, so much so, that Nagato couldn't sense it. Obito couldn't react to it as well, and was hit before he could even phase through. This is another factor. All Sasuke needs is a Rib-cage Coated with Enton. If Obito tries to touch it, he'll be toast. Amaterasu lit in the area would also prove to be quite problematic as well. Kirin is another game changer, so is Nagashi at close quarters.
Well, this is my take on it anyway.
