A mini-series in the same spirit as the recent "Iron Man-Thor" effort, or "Avengers Prime" could be really groovy.
Whether they can be friends is pretty much up to what flavour of crazy the Hulk is this month. Thor can have a bad day, but is relatively constant. The Hulk can go from mindless monster to fully Bruce Banner and every unpredictable temper in between. So, the mini-series would have to take place when Bruce is in a civilized frame of mind.
The story would be a tricky one. If the threat can be defeated with muscle, the plot will be over in three pages, tops. So, the threat would require their wits and experience to save the day. But the fans would have to see some muscle flexed. A tricky tight rope, but as said, a good writer would make it sing.
Yeah that could work. I mean Hulk isn't anything like he was back in the Savage Hulk days, and can be a dick. (see Hulk 622 with Skarr)