Even if it's a "lead in" to A2 it has to work as its own film. Having the Guardians come together just to lose would me them a joke in their own film. Having Thanos as an ally and stabbing them in the back at the end works as a more appropriate story telling device that's faithful to the comics and shows just how...odd of a villain Thanos is, which is a severe understatement. And like I said, having them defeat Thanos really diminishes his threat level come A2, even if he get the Gauntlet (which wouldn't make sense if they beat him...). Like I said, he'd be virtually Loki-level. That's not Thanos at all. It's just like Thanos to be shrewd and cunning, ally with the Guardians when it suits his needs, then turn right around and betray them when he gets what he wants, rather than fighting them. Really, unless the Guardians are in possession of the soul gems, which wouldn't make sense, Thanos has no reason to fight them. What would make sense is if the Church had them.