From what I've seen based on other cases:
#1. Never use a small/local bank. These guys are the worst and have generally pathetic or rarely enforced security policies in place.
#2. Do your banking off a boot disk if your not certain about your system's integrity. (Why are you using a questionable machine in the first place is a whole other story.)
#3. Try to avoid letting your business checking account get unnecessarily fat.
The fact is banks lose money. Going back to #1, most of the at risk banks in the United States are the small local ones (The FDIC is still regularly seizing banks.) Forget hackers, you could very well have $300k "stolen" out of your bank account if the FDIC shuts your bank down one Friday afternoon.
If you want to read more about this, I'd recommend krebsonsecurity.com. Brian Krebs has done a great job of covering this issue for quite some time -- in fact he has his own opinion of this court case written up now.