I'm assuming it was already in the water where you found it? if so, just letting it dry out will probably kill almost anything to be concerned about.
If the cinderblock/liner doesn't work, you could also just dig a hole and use a liner (if you have the yard space)
If it wasn't in the water, you could simply tie it to a stake and chuck it back in near where you found it (or a closer body of water) for the soaking, and come back and get it after a little while (plus, no need to worry about water changes).
for removing the dead/rotted wood, a stiff brush will probably work just as well as a scraper, and get in crevices/hard to reach places, and be less likely to noticeably mark the wood.