They asked you to put your carseat in an aisle? I thought that was prohibited.
Regarding the bulkhead issue, my experience on another airline (AA) was that the reservation agents did not know that car seats wouldn't work in the bulkhead, and they would recommend the bulkhead for space, etc. It's not surprising that this is also an issue at other airlines. I can't imagine that a flight crew would take someone off the flight solely because his or her child was throwing a tantrum, though.