There's no a priori reason that a fusion or fission drive has to have radioactive exhaust products. However, most if not all nuclear reactions are going to have radioactive byproducts, and if the working fluid for your exhaust comes into contact with the reactor it's going to pick them up. To cite an extreme example, the exhaust for NASA's NERVA rocket design was predicted to be highly radioactive, because the high-speed flow of liquid hydrogen through the fission core would actually erode the uranium fuel elements and expel particles of uranium with the exhaust, enough so that fuel element erosion rather than uranium depletion would be the limit on the core's working life. In order to avoid this, you need some kind of heat exchanger system to keep the working fluid for your reactor and the working fluid for your exhaust separate. On a conceptual level, this is what HEPlaR does. But- in the real world introducing a head exchanger into the system is always going to cut down on efficiency somewhat, because there's never going to be a perfect transfer of heat from one side of the exchanger to the other. As far as I can tell, FF&S assumes that by the time you get to HEPlaR TLs the exchangers are efficient enough that the loss is negligible compared to the benefit of not having your ship glow in the dark.
Of course, there's always the possibility of a starship operator antisocial enough to cut out the exchanger and get even more efficiency out of his drive, and screw whoever's underneath the ship when it comes down. Virus anyone?
Mweh. Heh heh heh...
-JTD
Any sufficiently stupid human is indistinguishable from a computer.