What happens when auto-pilot fails over the ocean? Let’s assume the current location puts the aircraft 2 hours from the nearest airport, but the destination is 2 1/2 hours away. 

Would the pilots hand fly the rest of the way? 
Are they allowed to fly to their destination, although it’s just an additional 30 minutes? 
And how difficult would that be (For the sake of the conversation, we can say I’m specifically asking about the 787, but I am generally interested in long distance capable aircraft)? Or is there tons of ways to fix the auto pilot? 

In short, what I’m asking is: how difficult it may be for two pilots to manually fly for this long, is it a big enough deal to cut the flight short 30 mins to land elsewhere?

I'm not sure under what rules, and not sure how the auto-pilot fails either.
As @Bianfable points out in the comments RVSM airspace is a problem but ignoring that for a minute: 

The question of will they continue? depends on the airlines op-specs. Different airlines will handle this differently and it may very well be handled different on different airframes within an airline. A call to base may even occur but there are lots of factors that can play into it such as what other equipment is operable.  

Assuming the Op-Specs dictate that the flight continues


  how difficult it may be for two pilots to manually fly for this long


Potentially not too difficult at all, most pilots trained in aircraft with no autopilot and all pilots are qualified to hand fly the aircraft. However after Op-Specs it is ultimately up to the pilot and they will consider many factors. Hand flying an aircraft in IMC can be a tiring task for even the best of pilots, a pilot may chose to divert or land sooner if they feel it would be unsafe to continue even if they are capable of flying the aircraft by hand.