I don't see why everyone concludes so easily there won't be enough atmosphere for aerodynamic control. The Kaman line lies at 100 km (official edge of space, the altitude at which the speed of an aerodynamic lifting body needs to be equal to escape velocity to produce sufficient lift to support it's weight, thus being in orbit, not in aerodynamic flight) Even if we very generously say LOHAN will reach 40 km altitude, this is not even halfway to that point. There is PLENTY of atmosphere to reach controllable aerodynamic flight (and in fact, if LOHAN is going to enter a proper glide it WILL reach those speeds due to simple dynamics)
Using full control inputs during rocket burn is not a good idea. Just like it isn't a good idea in any aircraft to use full control inputs at speed. However, a simple output scalar that limits the maximum control surface deflection as a function of indicated airspeed will be sufficient to solve that problem. The problem here is simply one of accelerations (g-forces) and the LOHAN design boffins should be able to calculate those long before the model is even constructed.