I have only just noticed that you are changing the names from common to scientific because you are starting to do the Australian snakes (all of which I am watching). You do have a good argument, although I do not fully agree. The problem is that you are not going about it the wrong way. Since it is policy, you should be first trying to change the policy before mass changes to the encyclopadia. The policies are there to create consistency. All you are doing now is making it more confusing. People expect to find the common names on Wikipedia, because that is the way it is done at the moment. Also, it seems you haven't read the Tree of Life guidelines properly. In it, it says that common names should be used where there are formal common names (such as birds) or there is a relatively unique common name. Otherwise use the scientific names. For example: White's Tree Frog is unique, and therefore the common name should be used. However, if you look at Litoria chloris, the common name cannot be used. Its common name, the Red-eyed Tree Frog has a disambigous page, explaining why that common cannot be used, and states that Red-eyed Tree Frog is not unique. 
The entire issue is trying to account for the most ammount of people. If someone wants information on a snake, writes its common name into the search box, and comes across an article with a strange latin name, they may be off-put and think they wrote the wrong name, and it redirected to the wrong place. Especially if the article did not have a photo. If a scientist wants to look at an article, and puts in the scientific name, and it is redirected to the common name, they will be aware of what the common name is. In fact, you will find that in most scientific papers, they will use the common name, stating the scientific name once in brackets so their is no ambiguity. A lot of articles use the scientific name because their is no common name. There is no other choice, and there is no problem with this. 
Please, bring this up on WP:TOL talk page before changing any more articles. You cannot create consistency yourself, and all you are doing is making it worse. If policy is changed other people can help, and it is possible to get all the articles changed. Policy needs to be followed, otherwise the encyclopaedia becomes a jamble. Thankyou.