For example one solution that I came across in the literature is by introducing a term in the NS equations for compensating the pressure fluctuations present in the flow (because of not having a divergence free synthetic eddy).
the best way to impose an initial velocity field that is divergence-free is to impose that every single synthetic eddy satisfies du/dx+dv/dy+dw/dz = 0. You can then simply sum their individual velocity fields at every point of your domain, when you generate multiple anisotropic eddies with random location. There are many examples of such model eddies such as Townsend's eddy (you can find the precise form in many turbulence books).
There is a fairly simple method to construct all possible divergence-free eddies.
Define a vector field. This can be absolutely any smooth function you desire (as long as it is differentiable). This means pick a function (analytic or discrete) for the x,y, and z components of a vector.
Define your eddy velocity field to be the curl of this vector.
FFT can do this job in Cartesian coordinates. I have a piece of Matlab code from some paper in JPO. It can decompose any flow field into the sum of a non-divergent part (curl of something) and a divergent part (gradient of something).
nft = 2^nextpow2(max(Ny,Nx)*1.2);% min 20% zero padding, Nx and Ny are grid points of the 2D flow field.