Googling this a bit more, I find it is a very common request. I think I understand the business reasons for not implementing this -- it would allow people to have great 2-way sync with a corporate domain email address which might cut into BES sales at the low end.
I did find an App in the App Store that basically allows you to Reply to an email through a different "Send Using", it's called "Forward Reply and Edit", and it's free under Productivity>Productivity. Basically, it creates a new email and stuffs all the senders and text into the new email, so you can then change the "Send Using" (since the BB thinks it's new). It's not perfect - it requires downloading the whole message, so there are download pauses if it's a longer message and you're on a shotty network.
Although it seems to work for me, the reviews seem a bit over the map, and I'm quite worried about being reliant on an app like this from such a small provider (although, the price is really awesome).
It's really too bad such a simple feature is lacking (changing the "Send Using" on replies"), but again, I guess I understand the business implications.