What you actually asked was "how is this worse," of course. If you want to fight this out on the basis that this idea is actually better, I'd have to see a detailed proposal before attempting to assign a silliness level. How did we get aboard in the first place; how come we can do it when the other cycles couldn't? Why are we putting soldiers aboard rather than one suicide bomber with a suitcase nuke? (I guess we can handwave that one since it isn't much worse than ME2's ending.) Why is killing Harbinger any more important than, say, killing Hackett?
How to get aboard: Obviously a small thermal exhaust port.
Why can we do what other cycles couldn't: Other cycles couldn't finish the Crucible either. Other cycles didn't get a lot of what this one did.
A soldier has to place the nuke. That's the sort of "suicide mission" I mentioned.
Now the question of why Harbinger is important is a good one that would require other changes. Had I been on the writing team, the Reapers wouldn't have been so unbeatable. They'd be stronger, but it would be a fight. Destroying Harbinger would be like taking out the Geth Dreadnaught, turning the tide of the battle. I know, I know; change one thing, change another, where do we stop?
Because it is sillier. Codex conveys that rapid indoctrination is a thing. Very first mission of the trilogy shows what live Reapers can do even from a distance and over a short time period. Arrival emphasizes that the Reapers can straight-up debilitate their foes in close proximity of their live technology. Leviathan emphasizes that measures must be taken to shield even a small piece of a Reaper. And the idea is to have Shepard and crew proceed directly through a Reaper body just fine in service of some conventional destruction method?
Sorry, but yeah, I'll take an overload wave, a digital upload in the vein of the virtual aliens, and some (optional) crazy particle neurophysics that use the mass relays at the very end over that any day.
The codex also says Rapid indoctrination causes decay in "days or weeks." What does the first mission show about Indoctrination? All I remember is that they heard a noise in their heads. Arrival shows what an Artifact does and no Reaper shows that ability. There's no reason they couldn't have it, but they just as easily could not have it.
Don't discount the "pride cometh before the fall" idea. While they have time to create contingency plans, they have no reason to do so. They purposefully set everything up in their favor. They had no real contingency for being blocked from entering through the Citadel relay. They had to FTL in. The Reapers think they know how events will play out. Remember in ME2 when they posited that the Collectors didn't detect the Normandy because they had no external sensors because they didn't expect to need them? It would be just like that.
The in-universe mechanics of the three ending options weren't the real problem with the ending.
Not in a way that the Reapers haven't thought of across a billion years.
There's no evidence they do much thinking. They have a plan that works every time. They already think they are the pinnacle of existence. Their cycle not working as planned is "beyond their comprehension."