There's always the bus.

Flixbus operates from Vignes/Cesar Chavez (across the street from LAMTA HQ) to Old Town San Diego. Fares range from $10-20 depending on when you go.

Numerous Greyhounds (take about an hour longer than Flixbus) from the 7th St. station in LA to National Blvd in San Diego. Fares around $21.

Amtrak not listed by WanderU, since obviously they're not running. The night bus from Bakersfield to LA to SD is a possibility if you're traveling in the wee hours and have a train somewhere in your itinerary (unless the state has ended that restriction). The do cost a lot more than the regular bus companies.

There are several bus lines running from points around downtown LA to San Ysidro. If you're looking for a Amtrak substitute that might not be a good fit.

Wondering what emergency triggered this. There was track work scheduled to the north this coming weekend (bus bridges between Chatsworth or LA and Oxnard) but this San Clemente stuff is a surprise. Metrolink and Amtrak don't provide details, nor does the news article which essentially does a minor rewrite on the Metrolink service advisory. Did part of the cliff collapse?