I'll have two structurally identical tables, one with old and new data, and one temporary table only with the new data, with which I'll make some further processing.
Is it better/faster to
load data local infile
When you say should I... that implies that you have some criteria. Do you need to make the import run faster? Or make it easy to write the code? Or preserve data changes you did in the temporary table?
I would probably favor
insert into <finaltable> select * from <temptable>.
But there's no right answer to this question. It depends what you are trying to accomplish.