When adding a machine to a domain through the console, the configuration service does not remove an existing machine account, although it will relocate it to the correct location if a non-default target folder is specified for the domain join task.
What the original poster has not bothered to mention is whether the client machine actually has managed to join the domain correctly (as easily determined by inspecting the NetSetup.log file on the machine), or whether this is simply a complaint about the fact a log message exists even though things are working properly.