My initial thoughts on encountering Christianity.SE for the first time were - "wow! this is really cool - I bet I can learn a lot here" & "This is such a great idea that I would really like to contribute to it" After browsing a question or two, I must have clicked on a link to a meta-question (no doubt one of the excellent ones about how to contribute on this site) and it wasn't immediately obvious to me that I had effectively entered an entirely different beast: I was somewhat dismayed that the list of questions on the home page weren't quite as interesting to me and that I seemed to face a catch-22 of requiring rep to do anything but having no means of gaining it. I was starting to think "this was such a great idea, but these crazy people are entirely focused on ridiculous nit-picking issues that have nothing really to do with christianity - how could I have been so wrong about my first impressions of the site?". I'm not sure how long it was before the penny dropped and I finally worked out how to go back, but I nearly abandoned my desire to contribute because of this issue. Would it be possible to make the distinction slightly more obvious and also to have a prominent link to rescue people from the rabbit warren?
There are already quite a few pieces in place to try to alleviate this confusion. For example the color scheme changes, the site title changes, and if you are a new site visitor the only color item on the page is a giant yellow box reminding people that they are not on the main site and offering a link back there:
I'm not sure how much more blatant you can make this without driving regular users bananas. Similar messages are in place for low rep users with extra reminders along the way. For example if you click to ask a question an meta, as a first time poster you will be walked through the difference between main and meta and have to acknowledge a popup prompt on the matter.
For experienced users with existing accounts and previous meta posts on other sites, these warnings are reduced and eventually it is assumed that you have the system figured out.
If you have specific suggestions to this flow in addition to the measures already in place feel free to suggest them over on the master meta site (as any changes would effect the entire SE network).
Just in case there is someone with exactly the same problem and they're reading this question, here's a link back to the main Christianity.SE site