Really I think that the relationship between hunter gatherers and farmers were good because they would largely be the same people. I really don't understand why some people appear to think the two lifestyles were distinct, even in current hunter gatherer groups the cultivation of food plants and animal husbandry is very common.
I suspect that what is being identified are changes in government and social organisation and because the focus on farming activities in the right climate can support greater populations. When human groups split, the divisions tend to be based on relatedness, this makes me thing that most groups would tend to be co-operative, and the rules that developed to maintain this would form the basis of intergroup co-operation. I also think that as groups adopted more agricultural practices and the population increased the shared decision making seen in many hunter gatherer groups becomes inefficient, larger groups need greater control, this control needs explicit rules or laws, and these require policing. The article implies a value system that favours the controlled and organised cultures based on agriculture, its debatable that this is in some way superior to alternative types of social organisation. All human groups develop a form of social culture its necessary for their survival.
The greater numbers of early agricultural groups require different cultural rules this and the loss of the sense of relatedness, make it difficult for the different groups to relate to one another and can even become a source of conflict in itself. However, it does seem that the most significant source of conflict among human groups throughout history reflects the need to control sufficient resources to maintain and possibly expand your own group. To maintain hunter gatherer groups, despite their limited populations, requires the control of large areas of land, while agriculture is more efficient they would still tend to gain population advantages.
I think that trade and relationships would be relatively easy, when the groups were familiar and there were few resource issues. Its often the case that humans develop social rules against the use of random violence, so the differences in beliefs and values are often used to dehumanise and justify killing their competition. It just seems inevitable that there would eventually be conflict, with the smaller hunter gatherer groups being eliminated or driven into isolated areas and this remains the case.