CalTrain, which would like to evolve from diesel-powered mainline-style trains to electrical multiple unit trains (i.e., a slightly scaled up version of BART) has studied the effectiveness of US and European safety standards, and concluded that the FRA's "build trains like tanks" mentality is probably not making passengers any safer; I'll excerpt a summary table:
|Impact Object||Speed||Probability||European CEM||FRA-Compliant|
|Steel Coil||20||Very Low||Marginal||Serious|
Collisions between passenger trains and freight trains are another matter--but could be avoided entirely by restricting freights to late night hours after CalTrain has finished running (this has been done elsewhere where light rail operates on freight lines), on the main SF/SJ part of the line. This would mean operating trains south to Gilroy with different equipment, but probably there isn't enough traffic to justify electrification of the south end of the line anyway.
Thanks to Peter Ehrlich for forwarding this report to the SFMuniHistory list.