I'm not the developer of the editors, we just use them because they are the best open source editors currently available. They each have their quirks so best to pick one that works best for your needs. If you think there is a bug in TinyMCE or CKEditor you can report bugs to the developers of those editors, but I suspect in this case the TinyMCE guys will consider their cleanup routines a feature rather than a bug.
In the Html content feature we have a setting to force a plain text area for those cases where you need to enter complex javascript and don't want to risk having the editors change any of it. But in the blog I would generally avoid use of javascript myself because it won't work in the feed, but if you really need to add javscript in blog posts CKeditor is probably your best bet and its best to save without switching back to wysiwyg view because it may run some cleanup when you do (though its cleanup usually seems a little more tolerant than the TinyMCE cleanup). Unfortunately TinyMCE uses a dialog for html view so there isn't a way to save without it going back to wysiwyg view.
So, in short, what I'm saying is I can't really do anything to change the behavior or fix bugs in the editors other than things they make configurable, any real bugs would need to be reported upstream to the developers who maintain them.
Best,
Joe