Native speakers probably won’t even notice the difference, since it’s a feature of English phonology that vowel timbre is mostly neutralized in unaccented syllables. The main problem is that if you’re expecting us to say [mae|dƷɪʃn], you will get confused when we’re speaking at a normal rate of speed and we inevitably say [mə|dƷɪʃn]. The schwa is the most common sound in English, so your comprehension will improve dramatically when you’ve mastered this one sound. A little effort will pay huge dividends.

It's definitely incorrect to say /[mae'dƷɪʃn/. It's unlikely that a listener would misunderstand you, but obviously you should aim for accuracy! Here's a link where you can hear three native speakers pronounce "magician" http://forvo.com/word/magician/#en

Agreed.

Hi, Native speakers will most likely not be confused, because not so many words sound very similar to magician, that may be mistaken for it. I can't even think of any word now :) However, the correct pronunciation is /məˈdʒɪʃ(ə)n/. Its pretty much the same thing as you mentioned above. I hope your question was answered :) Best regards.