here is one method, which assumes that B is supposed to span basically the entire domain of A.
Suppose the set of coordinates xa runs from Ainit to Afin, and that the row vector of coordinates B has N points, which are sorted.
w = (Afin - Ainit)/N;
xb1 = [Ainit-w/2 xb Afin+w/2];
E = sum((diff(xb1)-w).^2)
In this model the set of N points divides the interval from Ainit to Afin into N+1 intervals. E is the energy of springs of unstretched length w between each of the interior intervals (there are some details to take care of at the ends). The best set B is the one that minimizes E.
The ideal set of point spacings of xb is [ w/2, w, w, w ... w/2 ]. Other variations, that treat the end points differently, are possible.