no it is not, the only con to the A/T ECU is that the reverse lockout doesn't work. There is mention of this on HeelToeAutoIs it bad to use an auto ecu?
Source*Note that the use of an automatic ECU in a manual TSX will eliminate the function of the reverse-lockout solenoid, which is a part that keeps the shifter out of the reverse gate when you are moving forward. It is possible to move the shifter into the reverse gate while driving, so care should be taken when shifting into 5th or 6th gear. Heeltoe has tested this product in the HTSpecTSX and found no harm to come from moving the shifter into the reverse gate while driving, and it is not possible to accidentally engage reverse.
I found a local pick and pull that had just gotten an 08 TSX (via Craigslist), it was A/T but I went and grabbed the ECU - only $33!