well its probably way too late to separate them. if you dont want the purple just cut it as low as you can and let the yellow do its thing. If you like them both just prune them equally so one doesnt take away from the other.

Thank for your reply. I will try to keep them equally pruned and hope they both survive.

Fruity,
That's kinda cool when you think about it. Two different color magnolia flowers looking as if it is on one tree.
They will probably be fine, I wish you could post of pic of it blooming.
I like the idea.