I had recent infection in my 5 gal barrel recently, so I did a few things. First I rinsed it out with a lot of boiling water, just to remove gunk, but maybe it helped kill some of the bacteria/mold that was in there. Then I used Barol Kleen, which is a strong alkali, and let that sit overnight. Rinsed out the barrel the next morning with water and a citric acid solution to neutralize any leftover barol kleen solution. Finally, I filled it to the brim with a citric acid/sodium metabisulfite "holding" solution that I'm hoping is both killing any leftover bugs and preventing them from coming back. I've yet to fill it with beer, so I can't say if my procedure worked.
In your case boiling water would kill some of the bugs at first , but as soon at the temp drops below ~140F then the bacteria can get going again so water probably isn't the best. The barol kleen stuff seems like it should help, but it will strip away some of the character. Something in between would be alcohol, any neutral spirit (vodka/everclear) over 80 proof should work. You might not need 5 gallons, but it would be important to keep all the interior surfaces wet. So a few good shakes, or rotating the barrel often would prevent you from having to buy 5 gallons of everclear.