Caltrain electrification makes sense for all of the operating reasons you talked about. They can run more trains, and their power bill might just be competitive with their diesel bill the next time oil prices go up. They can get rid of most of the locomotive-hauled trains (need to keep a few for Gilroy), making maintenance easier, and some of that stuff is getting really old (I remember riding on a test train of the Nippon Sharyo stock and a brand-new F40 in the 1980s). EMUs may be long-lasting in general, but they will have a real job of it to beat the longevity of some of what Caltrain uses now.

As for emissions, electrics are certainly lower (near-zero, if you don't count reentrained and brake dust) local emissions - no more diesel fumes polluting the houses and schools along the tracks. GHG emission changes are incidental - Bay Area has a lot of hydro, solar, and wind power available on the grid, so the full-cycle emissions of the electrics will be reasonably clean - but anybody trying to quantify the benefit of that as justification for electrification will have a hard time - the justification is for operational reasons not emissions.

Then there's the elephant in the room - HSR, which provided a lot of the money for the job on the grounds that if they ever get to San Jose, they'll run the rest of the way into SF on Caltrain.

So, many reasons for electrifying Caltrain, some better than others. EIR and similar documents, still available at Caltrain's web site, cover a lot of it.