Please DON'T make this an option in the preferences, just make the right choice and do what the user expects.
The solution is pretty straightforward:
1) If the user already typed a back tick, use back ticks in the completion
2) If the user did not type a back tick, do not use back ticks in the completion, except if back ticks are needed
It's trivial to check if back ticks are needed: Just see if the identifier matches the regular expression "[a-zA-Z][a-zA-Z0-9_]*", and check it against a list of keywords. Make sure you quote only those keywords where quotes are necessary. For example "SELECT name, date, text FROM events" is perfectly legal, no quotes necessary! See
http://dev.mysql.com/doc/refman/5.0/en/reserved-words.html
If Sequel Pro would do it this way, it would just work for those who quote everything and those who quote only what's necessary.
Jakob
PS: If you don't believe me, just type this into the custom query window:
create temporary table events( name varchar(255), date date, text text)
MySQL requires a lot less quoting than Sequel Pro might make you think!