Yes, the "but" would be connecting two independent clauses. If you are confused due to the subordinate clauses (if statements), you can always move them to the end of the sentence to see itif you have two independent clauses to connect:
"I would not recommend that you watch this film if you have a weak stomach, but this film will be perfect for you if you have no problem seeing blood and guts."
I would omit the word "then" in either case as you have already set up of the case for arguing that the film will be perfectit is unnecessary.