It's not advised to eat a rune whole. You can bet it's one of the first things that someone did when runes were discovered. In it pops. But the result is anticlimactic: runes don't release any magical properties while they're in there. Earth runes won't magically solve any gall stones; an astral rune won't bless your small-intestine as it worms its way southwards. Then there's the whole 'exiting' thing: passing a rune is not particularly pleasurable.
Crushing a rune beforehand, though? That's slightly more likely to create magical side-effects. Having control over those side-effects, however, is a whole other matter.