Are you sure you aren't overdramatizing it just a little bit? And that is something of a feat because Gosho already puts a lot more romantic melodrama in DC than is required, .
Honestly, I've probably seen that scene where he first utters "Edogawa Conan" several dozen times, if only because of the movies, but in no way can I imagine any theoretical dagger going into Conan's heart at that point. He seems more amused by it than anything. And after that, probably all the way to Desperate Revival, he rarely seems to be affected by his own lies. Whenever Ran is close to finding out, he's more worried about her reaction to having taken a bath with him than anything else. Off the top of my head, the only times I can think of when Conan actually looks sad about his situation with Ran are when he turned back first (the first Heiji case, I think it was) and the end of the Desperate Revival arc, when Ran comes close to crying. Most of the rest of the time, he just seems irritated, but nothing close to having "the dagger with the venom of guilt and loneliness" stabbed into him.
Now, for Ran, you may have more of a point, since every time anything goes wrong, she just thinks "Oh, Shinichi, wherefore art thou not here?" Even then, though, your dagger analogy is too much. It's not as if not having Shinichi around prohibits her from living her life normally. Sure, she misses him. A lot. And she cries about it, too, but when, most of the time, she's acting just fine, the whole "venom of sorrow and longing" analogy goes too far. If you're going to suggest that she does feel bad about it, but doesn't show it, then you're using the same logic as some of the improbable pairings, whose fans just get some vague hints from here and there and pretend that two characters are in love with each other.
Now, I don't think anyone can seriously deny that Shinichi and Ran want to have a romantic relationship (and DC will pretty much certainly end with them together), but you're making it sound like the sky will fall upon us before they can change their minds, which isn't really true. Sure, they definitely like each other, but it's not some sort of eternal, "they can't live without each other" thing.
I can't actually argue with the rest of your post, mainly because I don't care about AiCon either. I'd actually prefer if Shinichi went all romanceless Holmes-like, with Haibara being his wittier and more useful, but much harder to impress Dr. Watson. (I guess that counts as AiCon, xD)
But I suppose it's more likely that he'll fall for Ayumi than that he'll stay single...