There's probably no "set this option" way to do it, but I've noticed that a.) the unread count is the number of unread messages in your inbox, not in subfolders and b.) iOS does not automatically check subfolders for new messages unless those subfolders are set to push via Exchange. So, if your work account is an Exchange account:
-Make a subfolder in your Inbox
-Create a server-side rule to move all messages to that folder. This can be done in Outlook on your work computer (assuming it's a PC) or probably in the Exchange web client (possibly requiring IE, since they disable certain functionality in the web client for other browsers...).
Then you still have access to the messages in the work account (+1 tap, but it's an iPhone 4, so it's snappy), and they won't show up in your unread count.