If you're just starting out with Colemak, I highly recommend for the first two weeks when the error rate is very high to keep the Caps Lock key mapped as Backspace. Afterwards depending on your usage pattern you'll be able to decide yourself better for yourself if you prefer it to be as Backspace or Ctrl.
Although I came up on my own with the idea of placing Backspace instead of Caps Lock, I wasn't the first to think of it. I found out that the Space-cadet keyboard, the keyboard which influenced the design of Emacs, also had a "Rub out" (Backspace) in the Caps Lock position.
Emacs out of the box is not very good from an ergonomic point of view, as it uses many shortcuts that might lead to strain on the hands, and using Emacs involves a lot more finger movement compared to Vim. That said, Emacs is a very powerful and infinitely configurable editor, so that aspect can be improved upon.
Under normal Emacs usage with a normal error rate, I estimate that people use the Ctrl key about as often as they use the Backspace key. But even full time programmers don't spend 100% of their time on Emacs. The Ctrl/CapsLock switch benefits mainly Emacs, but the Backspace/CapsLock switch benefits all applications.
If you're just using the left Ctrl key, try to get into the habit of using the Ctrl key on the opposing hand, which will reduce the need for the CapsLock/Backspace exchange.
I think several Colemak Emacs users have mentioned before that they switched the two. As I said, give Backspace a chance, and if after a while you see that you still prefer Ctrl, then go for it.
Here's an article about the MacIvory keyboard that advocates the Backspace in the Caps Lock position for Emacs users.