It's no different than building a framework in regular script code outside of the extension capsulation. The bonus of doing it with extensions is that you don't have to worry about adding code units to new projects just to use the framework. It's "built in" to the environment.
True, debugging when a problem occurs within the extension code can get a bit painful at times... but if you do rigorous testing of your extension code before encapsulation, you can minimize that.
I think, however, using JScript for extension coding has some advantage over VBScript. And, if SmartBear adds support for full JavaScript in the extensions, then there are some advantages that come along with that as well.
In any case, while I see your point, I think it can be mitigated with better coding practices all around. And if you want to go more compile time checking, then you can use the TestComplete SDK and build compiled plugins which would be in line with what you're looking for.