wavelength-based IFU data cubes VS velocity-based IFU data cubes
Your logic seems entirely correct. Whatever you do is an approximation, the difference between a Gaussian profile in cube B and what it "should" look like will be small for any sensible resolution. By sensible, I mean if your wavelength/velocity axis covers many resolution elements.

However, there is a "correct" way. Generate a Gaussian in wavelength space $f(\lambda)$ (if you think that's what your LSD is, where $\lambda$ here is short hand for $\lambda - \lambda_0$, the separation from the central wavelength) and then convert to velocity space in a flux-conserving manner: 
$$f(\lambda)\ d\lambda = g(\log \lambda)\ d\log \lambda$$
$$ g(\log \lambda) = \lambda f(\lambda)$$

Maybe a better way to do this is to get some data, like an arc calibration and see how unresolved lines look in your observational space?