There's nothing wrong with using grade crossings when starting up a low-volume line. It's more important to spend whatever money is still available to get access to Larkspur, Windsor, and possibly Healdsburg. Later, if demand grows to where many more trains need to operate, grade seps can be added piecemeal. Many light rail lines have been developed the same way.

As I see it, SMART never was aimed at "southern Marin" traffic - that's well-served by local and GGT buses, and the RR alignments are long converted to other things (with a few isolated exceptions). The regional purpose of SMART is Sonoma-Marin traffic and some Sonoma-N.Marin-E.Bay (via bus transfer to BART, unless a ferry to Larkspur can start up). Essentially, it replaces some of the GGT base service, with a little extra for inter-county commuters, and most important it's not on the (parking-lot at commute times) freeway. The "good points" in the IJ comment are simply another troll of the standard train-haters' points.

SMART is built. They're working out the final details for operation on the first segment and finalizing funds for the Larkspur connection. It's not going away now, so think about how to use it appropriately.