So you have MT running on the restricted domain? You could probably set up a proxy on the front-end server to pass requests for mt-comments.cgi through to the restricted server.

I wanted to have two blogs, one for each of my two domains, and since I didn't know any better, I installed MT twice.
Then the updated version (2.11) came along and I realised that this was a good time to try out the "Create New Blog" function. I did the export/import thing and got both blogs up and running in no time. One blog is restricted access (both read and write) and one is readable by everyone (BonkBlog). It's great, now I can log in just once to write entries in both blogs. And, I now have only one copy of the cgi-scripts, which means less hassle with upgrades.

The trouble is when someone else (that doesn't have access to my restricted blog) wants to add a comment on the open blog and the java-script wants to run mt-comment.cgi from the restricted domain. What should I do? Have a separate copy of mt-comments and mt.cfg in the open domains cgi-bin folder? Should I have two separate MT installations?

Yes. I was thinking about this on my way home from work and decided that there really wasn't any reason to do that since MT requires a login too.
Anyway, both domains resides on the same server, so perhaps if I read the Apache docs a bit I could do that proxy thing.
I temporarily (Yeah, right. We've all done that, eh?) solved my comment problem by copying mt-comment.cgi, mt.cfg (with a change to the cgi-path) and the lib-folder to my open domain.