It depends on if Toyota prewired the van for the non-jbl system. I know the Camry's and Solara's with the JBL package come with an additional harness that is prewired for the non-jbl system. You'll have to pull out the CD player and see if there is an additional harness tucked away back there.
Here's a thread on how to bypass the amp if you have the additional harness.
http://www.toyotanation.com/forum/t70082.html
If you don't have the harness there, the way I would do it is just run a new power wire with an inline fuse in it from the battery. Tap into an accesory wire such as the cigarette lighter for the acc lead. Run a new ground wire and ground it somewhere with bare metal, you might have to run it through the dash to the kickpanel to find a good grounding spot. Then run new speaker wire from the CD player to the speakers.
This way the old system will be left untouched and if you ever sold the van you can re-connect the factory headunit easily.