The second thread suggested using AppleScript. I've done some with it - not much, but it seems to me that AppleScript wouldn't be capable of doing all the things MathType does...
My understanding is that the iWork suite uses a file format that's meant to be easy to extend with plugins... Originally it wasn't going to be a suite, but a single application that just had a canvas you could drop any media elements into, and that any elements it didn't understand out of the box could have plugins written for them. Was that idea just scrapped entirely, or has Apple just failed to release any documentation on how it works?