In the sentence "This is because they have already gone gone home," the main clause is indeed "This is" with an implicit complement of "true" or "correct." The "this" is being used as a substantive representing something said previously.
"This is because Y" means "[The previous statement] is [true] because Y." No native speaker will wince at "This is because Y."
Although it is grammatical, it is very informal and wordy in style. I would be very unlikely to write (except as realistic dialogue)
"X. This is because Y."
Instead I would be likely to write
"X because Y." But people do not necessarily speak in the way that they should write.
As for the second question, where A and B are independent clauses
"A and then B" is not punctuated as I would like, but "A, and then B" is perfectly proper English. "Then" is being used to indicate a temporal sequence.