WYSIWYG Editor Messing with URL's
I feel your pain. Using wysiwyg editors to write emails is like using salt to heal a bleeding wound. It might have a purpose, but probably not in this context. and in this context, it hurts. A lot.

Anyway, back to your question: are you having the replacement in the href or "only" when you leave the link as part of the text you send?

The latest version of civi should behave correctly, otherwise, you can disable the replacement of the &amp; into &amp; (I've done it, it's not 100% html strict compatible, but seems to work fine with 100% of the real mail clients): here's an explanation on how to do it:
Escaping quotes in ckeditor breaks smarty-syntax

and a more generic question about how to disable the wysiwyg editor:
How to disable or fix the wysiwyg editor on civimail