It's possible to have an ECU get taken out by a alternator. I just helped a fellow IA member down south and sure enough his ecu was taken out. As soon as i got there i told him possible causes were cheaper alternators from say autozone. He just so happen to purchase one just recently. We swapped ECUs on the spot and sure enough his swap started right up. I have seen cheaper built alternators take out ecus and it's quite a shame. Apparently , Honda engineered theirs in such a way that when the component fails it will not take out other components on your vehicle. Not saying this is the case for your scenario but this is why i go with OEM, with some of my parts.