An important question, I think, is "What is the intention behind the Canons?"
There is a reason we call the Book of our Canons "The Rudder". They are not "laws", but rather, "guidelines".
Personally, I think the Canons, in condemning prayer with the heterodox are trying to convey the importance of not making Heterodoxy appear to be equal to Orthodoxy.
I often find myself in situations where the "the spirit of the law is more important than the letter of the law". For instance, I have attended Christenings, Weddings and funeral Masses for Catholic friends. I even attended the Wedding and reception into the Catholic Church of a former Orthodox friend. The semblance of "praying with the heterodox" is quite clear in such instances. But Love is, in my estemation, the Higher Law.
What do we do? The world is a mess, and sometimes we just have to do the best we can in the circumstances.