Considering Zack's track record with bullets and grunts, I don't see Zack fairing too well if he were caught inside the Shinra Building trying to rescue Aerith
Sephiroth held a respect for Zack as a fellow SOLDIER,which is why he attacked Zack so mercilessly and treated him as a threat who needed to be killed. I think that if they crossed paths again, Zack would do the same thing again, regardless.
I don't think Zack would've faired much better at protecting Aerith either. She'd have just died a different way. I can just imagine Zack fighting to protect Aerith and Sephiroth kicking his ass, and while he lies beaten, bloodied, and broken, Sephiroth kills Aerith right there in front of him, and then just flies off.
As Shikamaru also stated, Zack would've had a serious hard time picking up the trail of Sephiroth seeing as how he wasn't a true Sephiroth Copy, he wouldn't have the help of AVALANCHE, and he would not have much of a group to help him. It'd be hard.