One other option you have is to set up your account through BIS and have it not forward emails to your BB by default using the filters, and then whenever you want it to forward them you can just set the filter(s) to forward and it will do so until you change it back. Won't work for every application and it isn't like the gmail app but some people use it this way.
Speaking of the gmail app, you may be able to create a gmail account and have it access your work POP email and just use the java app to pull up the account. That is an option worth looking at and I know it works for one of my POP accounts.
BES 4.1.6 Exchange 2003 SP2