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.
Alone, This is because they have already gone home means nothing; it’s not even grammatical.
In Blah lah lah blah. This is because they have already gone home, what exactly does This is… contribute that justifies it’s being a main anything, please?
Meanwhile, would you mind separating those rather different subjects into two different questions, please?
– Robbie Goodwin Sep 29 '17 at 20:48