Softails like the Deluxe do not have catalytic converters in the head pipes like the Touring models do (the cats are in the mufflers), so changing head pipes isn't going to help.
If the bike is actually shutting down completely, and not just the rear cylinder at idle, then you should contact H-D, not the dealer. Many dealership people prefer to blow off customers with the "normal" or "they all do that" BS versus actually doing any diagnostic work. If the engine is actually stalling, it's a safety defect and you might want to approach it that way with H-D.
A good professional tune will help not only the excessive heat but will also make the bike run better and smoother. Even if you have no plans for any other modifications, a good tune performed by a fulltime professional tuner (not the average Harley shop) will be money well spent IMHO. Let the members know what town or city you are in and I'm sure they can offer names of reputable tuners in your area.
Since you are shorter of leg than some, it will be harder to get your leg away from the hot exhaust pipe. You may need to add deflectors to the frame like those on the Touring models to keep the heat off your thigh, or have the pipe wrapped. Wrapping the pipe has drawbacks, such as a tendency to promote corrosion or "rot" of the pipe under the wrap, but it would still beat the heck out of burning your leg on a regular basis.
Welcome to the site, and don't hesitate to ask questions. There is a lot of knowledge and experience around here, and folks are more than willing to help out.
Jerry