This is a suggestion from someone who has never had this problem, so no guarantees!
You don't say anything about the source of the soil inside your boots. For example, it is dried mud? Or is it perhaps the soil from years of wear, that is buildup from sock gunk and dirt marinated in sweat and then naturally dried, repeatedly?
Either way, I would experiment with warm soapy water and a toothbrush. Do one boot at a time. Use a mild hand soap to start, or if you are impatient, try one of the dishwashing soaps that specialize in attacking grease. I use Ajax Ultra Super Degreaser on my dishes -- it is a liquid and I often spill a bit on my hands, with no adverse effects. Use several drops mixed with warm water. If the handle of the toothbrush is too short, attach the handle to a longer rod or stick with strapping tape. Let the soapy mixture stand for say 15 minutes to soften the dirt and dissolve the oils.
For myself, I would not worry about getting the boots wet. My boots get wet frequently, from fording streams, plowing through wet snow, and splashing through mud puddles. It is what a hiking boot is made for.
Finally, I myself would not worry too much about getting my socks dirty: they can be washed. I would worry only if the boots were smelly.