Because it is indefinite, because he might have sought "any" presence, the right word is "a."
The word "the" would make the sentence confusing. "The sea" means, literally, all of the world's saltwater, all of oceans considered together. The sea is salty, the sea has tides, the sea covers 2/3 of the world. "The feminine sea" means all the world's oceans, regarded as having female attributes.
Since the sentence says that he "might" have sought this, it should say "would placate," not "will placate."
I'm not sure about your punctuation. I think what you have is acceptable. However, "a feminine sea, if you will," is a parenthetical phrase. I would probably set it apart with em-dashes:
"Living alone for a long time without wife and family, he might have sought for any presence--a feminine sea, if you will--that would placate his loneliness."
This is a case where a serious writer would check an authoritative usage guide, like the Chicago Manual of Style.