I ran into this because I was working on client-side templating, in which this can be a problem. jquery-tmpl for sure suffers from it (https://github.com/nje/jquery-tmpl/issues#issue/27).
Check-out http://jsfiddle.net/P2HEL/5/ first in any browser but IE and then in IE (I use version 8). The fact that it messes up the newline is an actual problem here.
Yes, you could use .text() instead, but the thing is that in abstractions such as templating libraries the code does not know if it is dealing with stuff that is gonna end up inside a pre tag (or any element with white-space:pre in that respect) or not. So I'd say it's something that .html() should be dealing with.
And also, from the .html() source I can tell that a deliberate effort has been made to fix problems with whitespace in IE. My test case demonstrates that I think this effort should be improved because it fixes the problem in situations in which the content starts with whitespace, but it fails to fix it if this is not the case.