There may well be a much simpler way, but it is really easy to both read and build the jdbc driver code. It can't possibly be much work to find where that exception is being thrown and just return instead. What the side effects of doing so may be on the product is another question entirely. Don't write long running queries and it shouldn't be a problem, though ;-)
I also wouldn't be surprised to find out that it is possible to modify mashzone's config in a manner which prevents the call to setQueryTimeout in the first place. Try explicitly setting the timeout to 0 or -1 or some other value that may imply infinity
