Ok I decided to do a little bit of a comparison between Loki's costume from Thor and his costume from The Avengers.
The first image is the preview from Hot Toys that was shown around the end of last year, which feature the outfit from Thor and the second image shows his fully armoured look from The Avengers.
As shown there are significant differences between the two outfits which easily provide a drastic enough difference for two separate figures.
The third image shows what i shall call Loki's casual outfit from the Avengers, comparing this to his armoured outfit from above the only differences i can make out are the addition of armour plates on his shoulders and forearms, the addition of the cape and a second "jacket" which looks to have armour plating as well.
Looking at this i would imagine we'll still get Loki from Thor because the figure has been made so it would be a waste for them to not sell it. If Hot Toys make Loki from the Avengers i'd imagine we could get both outfits in one set and we'd be able to display Loki how we wanted.