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What AFL needs is _instrumentation_ and of course the easiest way is to get that at compilation step, however you are not constrained by anything to get that part via other means. Check https://github.com/ivanfratric/winafl that uses DynamoRIO.

So, to answer your question -- it wouldn't be easy but it can be done.

The .NET Profiling API gives you a way to modify IL code before it's JITted, so that could be one way to do this. See http://mattwarren.org/2018/08/21/Monitoring-and-Observabilit... for a bit more info ('SetILFunctionBody() API')

I think there are Windows and VM-based approaches, but it probably isn't to difficult to mimic what AFL does on the CLR.