Working with a professor who does both mainstream and non-mainstream physics research I'm currently an undergraduate physics major in my final year at a US institution; I've recently finished applying to physics graduate schools for theory. With one of the schools in particular, I'm facing a bit of a dilemma: 

Within said school there is a professor who is very well known and well regarded within the field of my utmost interest. What's more, said professor is still doing interesting research within this field and as such I would love to work with them, especially given that this field tends not to have dedicated research in many US departments. 

But at the same time, this professor also does research in a non-mainstream, but not to say crackpot, field. That is, it's perfectly legitimate research but it's not mainstream. There are very few people in the US working on this particular subject and it's often looked down upon by people working in its much more mainstream competitor. While I think the subject itself is pretty cool to learn, I don't want to work in it by any means.  

As such, do you think it would be potentially harmful for post-doc applications or general physics academia related career goals if I end up working for this professor? Would working for said professor also associate me with the non-mainstream work, even though I don't want to involve myself in it whatsoever? Would there necessarily be any kind of negative impact? 

Thank you all very much in advance!
A well-established researcher usually has multiple research programs that are loosely united under one common theme. As such, they will have different reputations in different circles of academic research. A professor, for example, may be well-regarded in computational chemistry, but his work in biological modeling may receive little attention. Since a researcher in computational chemistry will probably not follow the literature in biological modeling very closely, the computational chemistry community may actually know little about the said professor's work in biology. Thus, to answer your question, how you will be judged depends on which of the professor's research program you are associated with. If you are really concerned, then you can simply stay away from the non-mainstream research that the professor is working on.

With that being said, I want to push back a little bit on the assumption of your question. It is sometimes joked that the sign of senility in a biologist is that s/he starts to work on the problem of human consciousness, which for a long time was not regarded as proper research subject in biology or psychology. But if the "non-mainstream" research that you are referring to is not downright unscientific, your concern may not be well-founded. Sure, as a young scientist it is not wise to work on unpopular subjects, but the popularity of a subject and the fad associated with it is not always correlated with the soundness of an area of inquiry. Sometimes good science is just not popular (such as Mendel's work that laid the foundation of classical genetic analysis).