Along these lines, why do each of us individually do pretty much nothing, or at best something pretty minimal, to help the millions of people in the real world living in poverty or dying from preventable diseases? It seems to me our empathy has only a "limited range", something like the "monkeysphere" effect I suppose, whereby we only really care about those closest to us. We have some abstract empathy for the less fortunate, but not enough to really do much about it.
I can imagine also that empathy asymptotes to almost zero at the emotional distance of simulated people (and that we can only think about large numbers of people logarithmically, so that there is hardly any difference between millions and trillions of people to the empathy portion of our utility function). As the scenario demonstrates, it seems like this behaviour has great survival value.
And to answer your question, the real world demonstrates the answer. The amount of foreign aid given to developing countries is abysmally small compared to the value we should place on the lives of those living in disease and poverty, if we indeed cared about them anything like as much as we cared about those who affect our lives more directly. The current amount of foreign aid given is more closely proportional to its UN and local PR value. It is politically, not morally, motivated.
For the second question, well we are generally more adverse to direct negative intervention that to lack of positive intervention, such as in the case of the runaway train that is about to kill a group of schoolchildren, and a big fat man either a) happens to fall in the path of the train (stopping it), but you could intervene and save him - but this would result in the deaths of the schoolchildren; or b) you are in a position where you could push the big fat man in front of the train, thus saving the children but killing the fat man. Most people would not save the fat man, but they would not push him in front of the train either.
I expect the explanation for this is that killing people for the immediate benefit of the group destroys social cohesion, since those in the group live in fear of whether or not their comrades will suddenly turn on them for the benefit of a naive kind of global utility. Likewise eliminating most of humanity for the benefit of said countrymen doesn't seem like it could be done without similarly introducing extreme suspicion into the remaining society. This problem is less evident with the foreign aid situation, although of course the possibility that no foreign aid might easily extend to reduced domestic aid might erode trust in those furthest from central power.
Letting the simulated people suffer is not likely to induce similar social chaos, unless perhaps the aliens can convince the citizens of the Earth that they themselves might be the simulated ones.
"Maladaptive" is subjective though. One's utility function may be such that their utility is only increased by explaining/understanding things. Of course if you mean that this drive supercedes eating and drink (I exaggerate), so that you undermine your ability to increase this utility in the long run, then I of course agree.