Can I drain the main sink in a double sink (with a small disposal side) into the disposal, to prevent clogs from building up from food waste?
The only way would be to actually disconnect all the piping and reconfigure your set-up so that the disposer is on the "main sink" side. It should actually be fairly simple to do, but it is a lot of hard work on your back under the cabinet. Removing and re-setting the disposer is not rocket science but if you have not done it before or are unfamiliar with setting sink strainers you might want to hire out the job. 

1) disconnect all the waste pipes all the way to the trap

2) remove the disposer: disconnect power, disconnect dishwasher drain hose (if present), remove disposer body from disposer sink drain assembly (method varies by brand), remove disposer sink drain assembly (method varies by brand).

3) remove sink drain assembly (basket strainer) from main sink and re-install on small sink.

4) install drain assembly and disposer unit on main sink.

5) install new plastic waste piping to tie drains into the trap: measure twice / cut once, test fit all pieces hand tight, tighten firmly with Channellock pliers.

Tools/materials: screwdrivers, Channellocks, plumbers putty, adjustable wrench, flashlight