How would taking Moscow lead to the defeat of the USSR? It's just a city, the importance of which to the Soviet war effort as a transportation hub
is IMO overstated. All the fundamentals which allowed the USSR to maintain it's war effort - it's abundant supply of manpower, the preservation of it's war industry and the retainment of sufficient industrial resources (oil, coal, iron ore, alloy metals, Lend Lease supply) - would remain after the fall of the capital. Even a putsch against Stalin wouldn't change these fundamentals. In fact, the only way I can imagine the fall of Moscow having a decisive negative impact on the Soviet ability to resist is if it triggered a civil war between different Soviet factions, like the RCW of 1918, a most unlikely scenario in 1941.
In sum, it was IMO impossible for Germany to defeat the USSR in a single campaign, so your point is moot.
War is more than strategy and logistics-it is also a political activity. Both Hitler and Stalin often defended or attacked cities not just for their strategic importance [and some did not have much importance] but their propaganda/national pride value. The prime example here is Stalingrad. Hitler ruined the whole balance of his strategy in the south by wasting huge resources trying to take Stalingrad, and we know the cost-the total loss of 6th Army, and the smashing of several allied armies. The loss of men and equipment during and after Stalingrad made the retreat from Asia manditory, and made the whole German campaign in the east a failure.
Stalin too wasted resources on Stalingrad, but he had less to lose, as the long German left flank had too few men and guns. So although he too was as fanatical about saving Stalingrad as Hitler was in taking it, defending Stalingrad did have more strategic value to him.
IF Hitler had let Manstein take Leningrad
when the last defences were breached, then Moscow would have been much easier, for the left flank would have been secured, the link-up with the Finns achieved, any future threat from the Murmansk convoys averted, and the ability to supply at least part of Army group North via the Baltic sea/Leningrad would have relieved somepressure on the main supply lines for army groups North and centre. this would have made the Moscow push less hazardous, and easier to hold onto once it was captured. It was all win. But the opportunity passed quickly and so most of a whole army group [Nord] had to do "guard duty" for 900 days. Perhaps "guard duty" is the wrong term, because AG North were under severe pressure from the Russians nearly all the time, especially when strong assets were transferred south for the summer campaign in 1942.