With
permaculture, so much depends on your location that it is hard to say which one is going to be better for you, though I tend to think in terms of swales for your situation, so the drawing with parallel strips is likely the way to go. You are right to think that wind is going to be a major factor. Primary, though, is
water. You have a limited amount of rainfall, and you will want to catch this in well mulched swales, and have your fruit tree forest bands be on the downhill side of these swales. Next on your list should be access. In my mind, generally you are going to have your hard travel surfaces be just upslope of your swales, thus giving you maximum rain run off going into your swales. While cropping is great, getting your tree systems established is your primary concern. After that, the individual fruit
trees and groups of fruit trees will provide a better microclimate for growing crops in their vicinity. The roadways also gives you access to your fruit and your crops; the latter will possibly be upslope of your roadway. You might need to crop, at least in the initial phases, in the
swale or in the cover of growing trees.
If the wind is cross slope, it will run the length of your swales and thus it will have full run between your bands of fruit trees. This is not good for your cropping areas, and as a result you will probably want to interplant windbreak trees in hedgerows going upslope and downslope from your fruit tree swale rows. If this is the case, your first drawing, which is more of a checkerboard, might have some accuracy. Unless the checker board pattern is large, cultivating crops with machines would be difficult. By hand, though, the checkers could be as small as you like. The smaller they are, the more
shelter you a getting from intense direct sun (evaporation), and drying winds.
If, however, the wind is downslope or upslope then your existing strips of fruit trees would be able to be the windbreaks.
Generally, though, you might be needing to consider how you can compromise between the two, so that a modified checkerboard, one with access roads on the contour above your swales, but strips going downslope to the road as windbreaks/shelter, would probably be very beneficial in a desert system, though the checkboard might be more of an alternation between crops and windbreaks, with bands of fruit trees running across the slope below swales. If the wind in the area is very intense, the road might have to meander in order to stop it from having a direct path.