So much depends on which doctors are freaking out, how much blood is actually in your urine and your overall health.
A good transplant center will have you receive outside counseling regarding various issues so you can make an informed decision about donating. Also, a coordinator's job is to assist you in donating. I am not sure a coordinator would necessarily be able to answer your questions about unrelated bladder issues that might prevent you from donating. At this point, you shouldn't be too worried until you know what is going on.
If everything is clear, you forward the results and resume testing for a paired exchange program. If it isn't, you find someone else to enter the exchange.
Blood in urine can be from "external sources", a mild UTI or other bladder issues. It doesn't necessarily mean you can't donate.