Is lower wing loading safer?
Yes in general it's accurate to say that lower wing loading is safer, especially in the hands of a pilot with low experience flying in calm weather with an unreliable engine.  Flying in gusty winds and strong turbulence, there would be safety advantages to a higher wing loading. 

The basic idea of limiting the wing loading is to limit the stall speed and thus the destructive energy involved in a forced landing.  As the question suggests, perhaps it would be wiser to limit the stall speed, or to allow deviations from the prescribed minimum wing loading in the case of a demonstrated low stall speed.

However the Canadian regs may also be written with the idea of limiting the top speed too.  Exactly why that's a good thing is not completely clear, but in the US at least an ultralight must not be able to exceed 55 knots in sustained level flight.