It appears that it has a different origin - quacksalver - Kwakzalver in contemporary Dutch literally meaning "hawker of salve"
In the middle ages Quack meant shouting - as these people would be at the market-place shouting to hawk their wares.
And taken from: http://rationalwiki.org/wiki/Quackery
"Quack" derives from the 17th century word "quacksalver", in turn from
the Dutch word kwakzalver (hawker of salve). Both "quack" and "kwak"
originate from the Middle Dutch quacken (to brag or boast).
Quacksalvers would appear in town markets offering cure-alls in
bottles to anyone gullible enough to part with their money.
Although you are right about mercury being used in ways which seem odd to us now, this is not the etymology of "quack" .
Off topic: I can't resist telling this, but there was an old saying: "You spend one night with Venus, then you must spend four nights with Mercury" as mercury was used against sexually transmitted diseases by injecting it into the bladder, or via the urethra.