I'm still new myself (not to Java but to Flex) but I would think that your server side Java shouldn't have to change too radically - using BlazeDS and having the Flex stuff talking to your server-side architecture . You'd probably not be wanting to do a JSP block 1:1 mapping with SWF but rather make one SWF as a SaaS and have it appear as one embedded window in the web page.
Also, I don't know if you're into switching Java frameworks but JBoss Seam has a stack for talking to Flex. It's called GraniteDS and is found at:
It looks like on big SWF, forget about Spring framework, services around legacy servlets.
Will check out GraniteD