I guess this is mostly relevant for the B2B case, but there it is possible to have prices that require decimal places, ie. where the prices is a fraction of a cent. Would this simply require adjusting the DB schema? is this a topic on the B2B agenda?
another option would be a global option of a price divider, ie. /10, /1000, /10000 etc
I dont recommend storing decimals. Better what you already suggested as alternative use different precision for your stored prices. Then you have to change Money module \Spryker\Shared\Money\Converter\DecimalToIntegerConverter::PRICE_PRECISION, \Spryker\Shared\Money\Converter\IntegerToDecimalConverter::PRICE_PRECISION, to precision you using.