Why do you think the a/an rule is legitimate, but that, say, verb-subject agreement isn't? Both are pretty much universally followed, but can be broken for particular effect. If you allow a/an to be called a rule, I think you have to also say 'I am/you are' is a rule, too.

A/an creates though my favorite technical copyediting conundrum, which is that of which version of the article to use for the subject "SQL query". Some readers will vocalize this as 'sequel query', others as 'ess-queue-ell query'. If you write 'an SQL query' you will seem illiterate to half your readers, while 'a SQL query' is just as jarring for the other half.