I've always been suspicious to SQL queries that are automagically generated by some framework. And when I read this article on lengthy SQL queries it certainly was another gallon of gasoline on the fire. Sure premature optimization is the root of all evil and all that but there is also another important rule in software development; Don't do obviously stupid things. If you want to use a framework for data access, which is very common for productivity reasons, be sure to design your software so it is easy to replace the generic framework with something specific.
If you on the other hand end up with really large queries when you write the queries your self (I'm a stored procedure guy so I have a hard time even making up what kind of SQL query would end up being that large), but it is obvious what the solution is - Stored procedure.