I'm not going to claim that this is the most efficient way to do this, but I got it to work quickly going this route.

The purpose of this script was to provide a folder location for less-technically-inclined folks to place a .csv with their most current sales office information. Names, addresses, and numbers change from time to time. We made a mechanism to import their .csv nightly, so that our lookup tool had the most recent data without needing a developer for every minor update.

First I made a batch file that connects to the MySQL command line tool. In the same line that I call the connection, I also trigger a second batch file.

"C:\wamp\bin\mysql\mysql5.6.12\bin\mysql.exe" -u root -p(password_but_dont_use_parenthesis) < c:\AdminScripts\maketable.bat

The SQL queries in the second batch file are very simple as well.
Here's the maketable.bat contents:

use database_name;
delete from table_name;
load data infile 'c:\\wamp\\www\\drupal7\\sites\\default\\files\\file.csv' into table table_name fields terminated by ';' ignore 1 lines;

To break it down, the first line switches to the right database in a multi-database MySQL server. The second line wipes the current data in the table. *MAKE SURE YOU'RE CERTAIN YOU WANT THAT!*. The third line then repopulates the table with whatever is in the csv file, and skips the first line since it's the titles/headers in this case.

Then we set a scheduled task to trigger the first .bat file every night.