Dear Felix,
I am not sure to follow precisely your concern but I can make some comments.
You are claiming that you are eliminating negative current by choosing hoppings from x to x+1. This is not true. You do not have to do it in both directions. The current is well defined after you choose your hoppings and it can be positive or negative (Local current).
I also noticed that you are looking at the local current density through the wire and then plot the result on the site where the hopping starts. It is one way of looking at the current density.
Kwant usually plots the current on hoppings and not on sites. If you want to look at the current density on the cut, you can do the following.
1) Create a new system that contains the slice where you do the cut. The order of the sites in this new system will be the same as in the original (Tested on a square lattice. Needs to be verified on other complex lattices).
2) Pick up the wave function in the original system and choose the values on the chosen sites and keep the order.
3) Calculate the current using these chosen wave functions and the new system.
4) Plot your current density as usual with kwant.plotter.current
You can check the enclosed file for an example.
You can do the same for a longitudinal cut (instead of the transverse cut.)
I hope this helps,
Adel