I also have these accounts with ComSec and i've done a bit of research on the same thing, and while you probably have a better idea now considering this thread was made about a year ago heres my 2 cents.
You're right that the CFD interest rates are slightly lower (with ComSec) and you can get greater leverage through CFDs. But here are a few main things that you should take into consideration when deciding which approach to take:
1. You do not receive franking credits with long CFD positions but you do with stocks acquired using a margin loan. (which may make a Margin Loan a better approach in some long term investments especially those that you are relying on income through dividends)
2. For CFDs interest is paid on the total value of your position not just the amount borrowed, that means you are paying interest on your upfront contribtution. This is not the case with margin loans which are a line of credit (Again higher funding costs can make a big difference in the long term.)
These reasons and a few others (consider that CFDs are synthetic and do not entitle you to the same rights as ordinary shareholders such as voting, rights issue etc.) are probably why most people say that CFDs are more suited to short term investment approaches while a margin loan is more suited to a long term investment approach.
Any other ideas would be appreciated!