Currently Mechjeb reads terminal velocity in such a way that it doesn't work for FAR users.

I have exceeded terminal velocity with FAR (yes, on kerbin) It's really hard to do but it can be done. However, the Mechjeb utilities still will not limit the throttle.

This should be a trivial matter to impliment, considering that FAR can tell you the current terminal velocity saving calculations.

I was thinking it probably should be included, not integrated. Obviously, integrating it would be a waste of space.

BTW, does the plugin still require the latest dev branch or does it work with the current stable. (I hate having to reinstall my MechJeb plugins daily.

I actually wrote a fix for that, but it means I have to build FAR as a dependency in MechJeb and I'm not sure how that works if you don't have FAR/NEAR. Anyone know?

You know that I already wrote that month ago ?
http://forum.kerbalspaceprogram.com/threads/60933-Optional-MechJeb-Modules-%28August-2%29

Do you know if there is a way to get it included with MechJeb in such a way
that it only loads if FAR or NEAR is present?

Yes, by using reflection. But I will not integrate it. The plugin does that fine already.
You only have to install 1 dll for it to work and it's way cleaner, faster and easier to build.