The word is skunked at this point. Using it guarantees that readers are going to have to pause and refer to the context, and depending on the context it may not even be possible to confidently disambiguate. Luckily both meanings have ample synonyms.
According to Wikipedia's summary of the situation, the French are to blame for the ambiguity - no surprises there! ;) But if we're going to avoid Americanisms, the better way is simply to use the word 'milliard', which makes perfect, unambiguous sense in any language.
Oh, good point... Right, back to the drawing board - how about "kilocount" for a thousand, "megacount" for a million, and "gigacounts" for a (short) billion? The prefixes were apparently resurrected from the Greek for use in the metric system, but haven't had any other contradictory meanings as far as I can tell. I know I'm mixing up the Greek and Latin roots with "-count", but "kiloarithmos" is two syllables too many!
I'm not sure what his origin was for the term, but "skunked" as an adjective to me indicates a beer that was spoiled by exposure to light and/or heat. It's gone off.
Oh, how interesting - I had a personal 'eggcorn' interpretation that it was an elision of "and on" (which also makes sense in many contexts), and never connected it to the word "anon" in writing!