1. I'm surprised your partner & his brother ever got a 3 bed house - certainly wouldn't happen in many areas where Council 3 bed houses are in very short supply.
2. The tenancy is still in the names of your partner & his brother. Any change in that (such as his brother taking his name off the tenancy or you asking to go on it) automatically terminates the existing tenancy (that is the law - not a matter where the Council has any discretion) & therefore gives the Council the right to decide whether whoever is occupying the house can have a new tenancy.
3. Assuming the only occupants are you, your partner & the child you do not - under the rules used - require a 3 bed property so the Council would almost certainly refuse to give you a new tenancy. (The additional child will make no difference to this - the rules say they can share a bedroom until (I think) about 10 -12 yrs old.)
4. The same could possibly happen if you go to Court & lose. In fact, I cannot see on what grounds you could succeed with a Court claim because what the Council has told you is simply a factual statement which is a correct one.
5. Best option is to leave everything as it is (including the brother on the tenancy) until you buy.