Dreampanther
We all face the reaper.
Okay, I think I understand your point, and even agree - if Supes knows Loki is behind the attacks on civilians, and suspects that by taking Loki out the attacks will stop, then obviously he would be a fool not to.
Going back to the original scenario, my problem understanding the encounter is there are no details given for the fight. So, there are a few ways the encounter can take place:
One, kind of like a duel: Both are angry at each other, charge and clash, and Supes win because he is stronger and faster.
Two, Loki is messing with Supes for some reason, which means he knows about Supes' speed and strength, HV and ice breath, as well as his vulnerabilities to magic and Krypton - and in this case it will by no means be a walkover. In fact, I see Loki getting away with his tricks for quite a while - he can go intangible, invisible, open portals to bring monsters to help him, find magic weapons and armor to protect himself and hurt Supes - hell, he can probably even find Kryptonite somewhere, by making buddies with Lex or traveling through space and time to find it. In this version, I think Supes is gonna neef help, from the JLA or from Thor. Even Thor needed help dealing with Loki, once Loki actually set his plans in motion.
Third way, Loki is attacking Earth or trying to take it over or something, but doesn't know about Supes or Thor brings him through to Marvel Earth to help him against Loki. This seems the most plausible, and the most likely.
In this case, I see a pretty decent fight developing. Unless Supes gets lucky and catches Loki unawares, I don't see him taking Loki out that quickly. Loki likes his illusions, both in comics and the movies. He usually has a trick or three up his sleeve. However, in this instance I don't see him able to keep Supes down for very long, as he won't know about Kryptonite. He would be able to hurt Supes, sure, using magic attacks, but in the end Supes is a character designed to take whatever is dealt out to him. He'll survive, endure, and once Loki runs out of tricks, he'll take him down.
Still, it should be a decent fight...