I've got good news and bad news and I'm going to assume you'll want to read the good news first. In the one of the latest development releases of Bukkit 1.3.1-R0.1 (build #2301), the error where users got kicked when they used Tree Feller or similar abilities in MCMMO has been fixed. It was initially just a bug in Bukkit that when users destroyed a block that set the block (or another block) to air improperly, they were kicked.
The bad news is that any build above #2991 (I think) throws a shit heap of errors into the console regarding a deprecated event, as Tunes knows. If it didn't return the following error I'd be perfectly happy to test it out, but the "Server performance will be affected" pushes me away a bit.
The following error is from Factions, but it pretty much returns an error on every plugin.
12:05:31 [WARNING] [Factions] "Factions v1.6.8" has registered a listener for org.bukkit.event.player.PlayerChatEvent on method "public void com.massivecraft.factions.listeners.FactionsChatListener.onPlayerEarlyChat(org.bukkit.event.player.PlayerChatEvent)", but the event is Deprecated. Server performance will be affected; please notify the authors [Olof Larsson, Brett Flannigan].
org.bukkit.plugin.AuthorNagException
at org.bukkit.plugin.java.JavaPluginLoader.createRegisteredListeners(JavaPluginLoader.java:302)
at org.bukkit.plugin.SimplePluginManager.registerEvents(SimplePluginManager.java:507)
at com.massivecraft.factions.P.onEnable(P.java:112)
at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:217)
at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader.java:357)
at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManager.java:381)
at org.bukkit.craftbukkit.CraftServer.loadPlugin(CraftServer.java:263)
at org.bukkit.craftbukkit.CraftServer.enablePlugins(CraftServer.java:245)
at net.minecraft.server.MinecraftServer.i(MinecraftServer.java:296)
at net.minecraft.server.MinecraftServer.d(MinecraftServer.java:275)
at net.minecraft.server.MinecraftServer.a(MinecraftServer.java:225)
at net.minecraft.server.DedicatedServer.init(DedicatedServer.java:140)
at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:380)
at net.minecraft.server.ThreadServerApplication.run(SourceFile:539)