Does MT have any trackback-throttling mechanisms? EE has a couple of cool ones — one that allows you to set the span of time that must elapse between pings, and another that randomizes the trackback URL (the one that I think is most important), adding a one-use only random string of digits to the end of the address, which means that an actual human has to get and copy the URL manually in order to successfully ping you.
That’s the good news. The sacrifice is that there is no trackback auto-discovery function — if you just link to me, relying on your system to automatically ping me without using the randomized URL, I won’t actually get the ping. But… well, it was a small price to pay, I think, for not having to clear up all those bot pings every morning.