Do I need to write my own unmanaged IL library to rewrite IL with the CLR Profiling API?

Probably. It depends.

The Mono Project has a library called Cecil, which you can access here:

http://mono-project.com/Cecil

However it's managed code, which you can't call while profiling. You may a have a few options though:

1. Use IPC. You could spawn a new process, doing the rewriting using cecil in that process and then pass the bytes back to your profiler using named pipes.
2. Port CECIL to C++. The code's distributed under the MIT / X11 license, so you could do this without having to share your changes.
3. Just write your own stuff from scratch.

#1 introduces a bunch of extra complexity. Your profiler would end up having more moving parts than it really needed. Also, the IPC introduces a bunch of extra overhead.

#2 would take a long time. Given that Cecil is still only at version 0.6, it might not be worth the time to do it, vs writing your own implementation.

#3 would give you the greatest degree of control, and would probably be the most performant. However it would take substantially more effort than #1 would.

I wrote a simple one for OpenCover https://github.com/sawilde/opencover which you or anyone else for that matter may find useful