No, that's not currently possible. Well... unless you get very creative with weapon and make a system that fires an invisible torpedo into your own hull. You actually *could* do that, I'm pretty sure.
A self-destruct would be problematic because it would need an entirely new AI for it, too (and really, a player confirmation mechanism, or it'd lead to no end of frustration). When modding in new systems, you really have to build on something that's already there - at least to some extent.
Hmm... systems might be a good thing to open up AI modding for first.