Yes, but that was an utterly ridiculous requirement added by the Army Corps of Engineers. As were some very expensive bridges across swamps that already had perfectly functional railroad embankments. Neither were actually required by any reasonable interpretation of even the most strict environmental laws, and would not have stood up in court. The electrification was needed solely to maintain schedules, because the terrible design meant that diesel trains couldn't accelerate fast enough to reliably make schedule.
A properly-designed project with adequate double-tracking could use diesel power just fine. While large-scale electrification of the entire MBTA CR system, including South Coast Rail, may well be justified someday on other grounds (reduction in emissions, massively increased frequencies, use of NSRL, better acceleration, etc), South Coast Rail as it has been proposed in several iterations since the 1980s does not justify electrification for a dozen or so daily round trips.