Actually, unless your configuration options are doing something really obscure in the background or are interacting badly with another addon, there shouldn't be any significant impact, in terms of CPU time, assuming you aren't tampering with the options all the time. Granted, your UI will use more memory perhaps without good reason, but memory usage has become largely irrelevant, assuming your machine is powerful enough to handle Wotlk without many issues and your addons are not "leaking" due to bad coding.
It also depends on the size of your config LoD addon. That being said, a way to unload an addon could be quite useful regardless
