I would strongly suggest not trying to "not implement it his way".

So far, it sound like you have done the right thing. You were humble and brought up a counterpoint. I could not tell from your question whether you simply disagreed with his method, or you disagreed and presented an alternative. Bottom line though, always offer a clear and thought out alternative when you try to shoot down someone else's approach. As he might see it, you have a good idea that might work, and he has an idea that does work.

In any position, we are forced to do sub-optimal things all the time. If you really don't like it, then you can do as you did and bring it up. After that, its the boss' way or the highway. On the brighter side, you are insulated from much of the risk of poor decisions as a junior.