The quickest way would be to hire a car and drive from SD to LAX (about 2-1/2 hours). But, I'm guessing that you've already purchased your rail tickets or you'd rather not drive.
That said, the second-quickest method would be to take the train as far as Anaheim and get off there (rather than continue on to Union Station). If you've already purchased tickets to Union Station, you'd be forfeiting some fare, of course. At Union Station, take a 6 or 7 minute taxi ride to Disneyland Hotel ($15 including tip) and catch the Disneyland Express Bus to LAX. You haven't told us how many of you are traveling so I can't tell you the total fare for this conveyance.
The Union Station Flyaway Bus could be as quick as the transfer method I've described (or a little bit longer -- it has to do with what time the train arrives at Union Station since the Flyaway, leaves on the hour and the 1/2 hour and you'll need a few minutes to transfer from the rail platform to the bus plaza behind the stadium.
Of course, the Flyaway method is only 2 steps whereas the Disneyland Express bus method is 3 steps but you didn't ask for the simplest route; you asked for the quickest.
Another possibility is to take the train to Anaheim and connect at the station with a 'shared van' from supershuttle.com or redvans.com. This would save you the taxi ride but if there are only 2 of you traveling, the van will make 2 or 3 more stops to pick up additional passengers (since the vans carry either 7 or 9 passengers). If there are 4 or more of you, then the van will stop less often to pick up others.