The Oxford English Dictionary has the phrase "God rest you merry" from as early as 1534, centuries before the appearance of the carol.

Shakespeare also used it in "As You Like It."

It meant "God grant you peace and happiness!"

So case closed, comma-wise.

(Unless people want to sing about "merry gentlemen," which is their business.)

The authoritative OED also dates the carol to a "single sheet" of 1700-1701.

The phrase seems to have gone out of ordinary use during the 18th century.