I think the issue is that the bearings/bushings that hold the shaft are likely to have some kind of grease/oil in them. That probably wouldn't be a big problem at room temperature, but when you are pumping near-boiling wort through it, it could very well be hot enough to make the grease/oil runny enough that it could be more likely to make its way into your wort.
I don't know how big a deal it would be, especially without seeing the insides of your pump. Maybe there is little (or no) lubrication in your bearings/bushings, making it a moot point. If there is, perhaps it would be possible to clean them out thoroughly and use some kind of food-safe lubricant instead?