Hi YMF,
You're correct that "clearly" or "clearly then" are conclusory indicators. However, in a Main Point Logical Reasoning stimulus, you have to be careful not to trip up on the indicator words, which are often attached to an intermediate conclusion, and instead focus on the logical flow as a whole. So to break this stimulus down, we have:
Sentence 1: Premise telling us that bald eagles inspire sympathy for other species.
Sentence 2: Conditional statement that diagrams out to:
Bald Eagle Sympathy 
Political Will Needs of Obscure Species
The tricky part here is the word "clearly;" my guess is that this sentence is meant to be an intermediate conclusion, although there is a clear logical gap between this sentence and the preceding one, so it isn't a valid inference. The big takeaway should be that it is then used as a premise for the final sentence, which is merely a statement of the contrapositive of this logical chain.
Sentence 3: A conclusory statement that is merely a restatement of the contrapositive of the second sentence's A
C conditional chain.
Needs of Obscure Species
Bald Eagle Sympathy
This is a valid inference, and does logically flow from the second sentence, making it the main conclusion of the stimulus. Answer choice (B) paraphrases it, making it the correct answer.
Hope this clears things up!
