Two years after this question originally was posted, there is now remap-istanbul which seems promising.
you can read more about it in Sitepen: Code Coverage for TypeScript and Other Transpiled Languages
As they write in the Github project:
A package that provides the ability to remap Istanbul code coverage
information to its original source positions based on a JavaScript
Source Maps v3.
As I read the documentation, the project will take your istanbul-generated coverage as input for conversion based on the sourcemap. This sounds like an additional step, but I am sure it will benefit so that you can get rid of those transpiled autogenerated lines in the coverage report.
I believe this is exactly what you will need.
