All things considered this line is a better candidate for trail treatment (with some spots where it just won't work) than some others that have gotten it. The bridge ... I can see the City's point ... steel would be less subject to many of the insults a bridge there is likely to be presented with as part of a trail and over a homeless camp. A city as broke as SJ should definitely go for the lower-maintenance solution, and in cases like this they're usually using Somebody Else's Money (e.g. Fed) so the extra cost isn't really a big deal.

If you're really worried about the historical aspects of the bridge, take pictures and document it, then tear it down and put in something long-term useful. That's what RT did at Alder Creek (old timber trestle - documented it, left the now-unused stone abutments, then built a concrete freeway-type bridge that's much more suitable for transit use). Besides, getting rid of an old creosote-soaked timber bridge could be considered hazmat remediation (especially in a perennial creek).

The only other spot I saw in a quick Google peruse of the western part of the old line that had a significant piece still in place was the grade crossing at Monterey Highway(!). All gone on both sides, but rails and good-condition concrete panels still in place on the road with faded pavement markings (and no other signs). How many truckers see the tracks and come to a screeching halt only to find that it isn't really a railroad any more?