Depends on the survey involved. Most surveys are very superficial: did the associate greet you?, give you eye contact?, smile? etc. I would respond objectively to those issues and then drop a note to the scheduler stating pretty much what you have stated here. Some surveys are more in depth and may even get into the effectiveness of the interaction, which is where you could comment about distancing yourself and finding the odor distracting. Some surveys actually have a comments area where you can communicate the issue to the editor/scheduler and they can pass the information on tactfully to the company.
My usual issue is heavy perfumes which in their own way can be as noxious or more noxious than BO. When they distract from the interaction and the sales opportunity the client needs to be made aware of it and generally the best route is through the editor/scheduler so that you don't get knocked down on the 'objectivity' of your report.