So you've got a bigger than stock turbo and higher than stock boost. The ECU doesn't have enough range to eliminate knock by itself on a setup like that. The ECU is only really has enough control to save the stock engine in good tune with bad gas or maybe being slightly out of tune. It's definitely not enough that you don't need worry about how high you turn the boost up.
An electronic boost controller won't change what happened any. Providing it's set the same as the MBC you should still have the same boost at the same RPM or if anything more boost, especially under acceleration, because of the different operating characteristics of the EBC.
What you really need is to be able to log knock, see where it's knocking, tune that knock out and figure out when you need to back out of it on long pulls up hills and the like. I've got DSMLink in one of my cars and it's a great, easy to use, and quite powerful program. It's alot more money than just a logger tho, but a logger won't let you change anything, only view, DSMLink does both. I don't know much about the OBDII loggers because I'm a 1G guy. if you can get something that runs on a palm pilot that can be real handy, I mounted mine up by the dash vents and use it like a guage sometimes. It gives a real good idea of what kind of conditions cause knock and can give some other general feedback on your driving style/ECU operation as it relates to fuel economy, for instance.
A Wideband 02 sensor is also a great tool to have to monitor your engine tune.
Have you taken the motor apart yet to find out what's wrong? There should be some good signs in there of what went wrong. Which will in turn tell you how to keep it from happening in the future.