I have a way of finding all of the spawns under the lava that doesn't include killing yourself a bunch.
It involves editing save files though, so... keep a backup I guess.
All you have to do is load the save file and place a plate brick just below the surface of the lava.
Give that brick an emitter that is used no where else in the map. Something like... the wand emitter maybe.
Then save the bricks.
Open the save file with a text editor such as notepad.
Ctrl+F to look for that special emitter.
Just above the "+-EMITTER" line is the plate that you placed earlier.
Right after the #x#F" line there should be three numbers.
I shall show an example using letters.
1x1F" #A #B #C
You want to look at number C.
Copy that number down.
Then simply Ctrl + F again and this time look for "Spawn Point"
Once you find a line with those words in it look for the 3rd number just like before. If the number is less than the number you copied down earlier, delete the line.
But wait! You may have noticed near the top of the save file a line that goes something like this, "Linecount 14091"
You'll want to change that. So keep a count of how many lines you delete, and subtract that number from the linecount total.
And that's it. Hopefully, if by the time you're finished you didn't screw anything else up, the save file will work ingame, and all of the spawnpoints below a certain level will have been removed.
Keep in mind I have not tested this yet. I have to go to work soon and do not have nearly enough time to test it.