I try to always start replies in a new window for this reason.
I just do "File -> New window" then Back.
A "replying to" link would be useful so long as it specifies target="_new". Otherwise, we'll increase people getting burned by clicking on something during a preview and coming Back to find that your browser no longer displays your previewed content from the cache.
This and similar behavior became so annoying that I've set IE to "never" expire cached content (which is also annoying but still preferable).
And yep, I do instinctively open nearly everything in a new tab
Then what do you care what the default target is? In a reasonable browser, requesting that a link be opened into a tab should open it in a tab even if target="_new" is the suggested default behavior in the HTML of the link. This is how my copy of Mozilla behaves.
So the suggested feature would only affect you when you forget to open the link in a new tab. In that case, would you rather have a new window pop up which you can just close if it bothers you, or have the in-process preview be replaced by a new page with the risk that going "Back" doesn't restore your text from the browser cache and the node contents that you were composing are simply lost?
I don't find that design decision at all difficult (and I particularly dislike target="_new" in most cases).
Further, for this particular use, I'd find jumping between two tabs (only one of which can be visible at once) to be the wrong way to consult a thread while I was composing a reply to it. So, even if I were in the habit of opening links into tabs, in this particular case I'd make an exception and open a new window so I could view the original node while I'm typing the reply.