Tom:

True, Rutan avoids an aft-wing stall by purposely limiting the amount of "up" lift the canard can generate. This does prevent an aft-wing stall, but also limits the aft-wing from generating anything close to CL-max. This means you need even more wing, or more flaps, to get a reasonable approach or takeoff speed. More wing or more flaps equals more complexity and more weight, which equals more cost. (Both to acquire and to operate). Minor consideration on a homebuilt; more on an airliner.

If the canard (or foreplane) can be made to have a huge range of motion, an aft-wing stall with this configuration could be made recoverable by making the canard lift go to zero, or even a negative value, which would drive the nose (and AOA) down. On all supersonic fighters that I can think of there is an all-moving stabilator (instead of a horizontal stab and elevator), to achieve the required control moment-arms with the large center of lift-ranges generated from approach speed through supersonic flight.

All-moving slabs haven't been used on airliners because, I believe in part, they are more responsive, and would make for a rougher ride in an airliner. This same characteristic makes them perfectly applicable to fighters, where rapid g-onset (and pulling to CL max) is often a necessity.

Rick mentioned fly-by-wire. You don't have to make it that way (as above), but to get maximum benefit from a FSW jet with a canard, you would probably want to. A FBW system would make an all-moving canard stabilator easy to adopt without sacrificing ride quality.