The most straight way is to introduce another model for that non-master table. It’s not about just creating another AR class, but adjusting your vision of the problem domain.
Then you’ll be able to use has_many :through (if it will be still be needed).
Can I get more specific answer? 
I doubt you can without being more specific about your problem.
E.g, you have models A, B and C and a “non-master” table to link them together.
Then you can create model D that will represent some meanful entity in your A / B / C model. Then you can do “A has_many :bs, :through => :d” and vice versa.