The short answer is yes, I believe so, in fact it can probably be done in more than one way. Without experimentation here I can't give step by step instructions as to how to set the switches.
One thing that I expect to work is to enable LTI in course.conf for the course where you want LTI enabled rather than in localOverrides.conf. In that case the other courses will not be affected. Jason Aubrey or others may have more information. The LTI connection is relatively new and we may need some experimentation as a group to determine the best and most flexible way to set it up. Please report back if you find something that works for you.