If Zack had beaten Sephiroth in Nibelheim, I think he'd have been shocked and dismayed, angry as hell, etc. But I agree, getting beaten by Cloud, a lowly grunt, is so much worse.
I have to say, Sephiroth probably knew at least something about Cloud, rather than no idea at all who he was, since he did know Nibelheim was the kid's home town. Not that he had to have talked to Cloud to learn this, he did ride there in the same truck as Cloud and Zack after all, and being such good friends I am sure those two had to talk about it.
But, even knowing this tiny bit about him doesn't downplay his complete indifference to Cloud. It'd give him no clue about Cloud's excellent potential with a sword, or anything else for that matter. Remember when the bridge breaks on the way to the reactor the first time?
Sephiroth: I know it may seem cold, but we've got no time to search for them.
This line is in reference to the other MP who disappeared at this point. Sephy really doesn't give a shit about him. Sure, he's still basically polite to people, but he can't bother to take a few seconds to look around where they came down? If it had been Cloud, would he have bothered to look for him? Hell no, imnsho.
So I do think Sephiroth's hatred of Cloud is much greater than it would have been for Zack in reversed roles. There is a big difference between screwing up and letting a non-threat gut him and then throw him off the bridge with his own weapon, and getting bested in a real fight with a fellow SOLDIER. So, the relationship builds from there. The above mentioned fact that this sort of humiliation just keeps on coming just keeps stoking the fire. MP Cloud kills Sephiroth in an unimaginable burst of strength and rage. Puppet Cloud snips his strings and kills Sephiroth again, both physically with his friends and in a one-on-one duel of wills, refusing to have his strings tied back on. Depressed As Hell Cloud gets pissed and chops Advent Sephiroth up with Omnislash 5/6. Every time, Cloud is seemingly an underdog for one reason or another, and every time Cloud manages to pull off one big moment (Throwing him off the bridge, Getting his weak-ass mind put back together by Tifa, Getting his motivation back so he had enough power to limit break) that throws it all out of whack. Zack was an underdog too, but never as big of one as Cloud tends to be.