It is harder to prove to the ATO that you are carrying on a business of share trading than otherwise, so I doubt you would have a problem if you treated the sales under the normal 'shareholder' CGT rules.
Personally, unless you have very complicated tax situation, i would give the accountant the flick and use e-tax...did my tax on etax in 2 hours last year and i do LOTS of share trading, have a couple properties, managed funds etc, and a full time job. I find it easy.