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 if 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 it is unnecessary.