The Dictionary.com definition of kludge:
a software or hardware configuration that, while inelegant, inefficient, clumsy, or patched together, succeeds in solving a specific problem or performing a particular task
I would not personally say that CLR is inherently inelegant, inefficient, clumsy or patched together. That you can write poor code with CLR shouldn't be evidence of it being a kludge. People can write bad code in any language.
Certainly the judgement is in the eyes of the beholder and I can understand why someone with a lack of familiarity with .net languages would find CLR to meet the definition of a kludge. I just disagree that is inherently such.