Hi J K,
Hm.... this has become a problem for many students since the news has come out, to change the criteria of admission for IIT-JEE. It has been planed that maximum criteria would be given to the 12th Board results as compared to the entrance exam for IIT-JEE.
See as you might be knowing that anything to be implement in India takes a lot of time and you never know it might take even 4-5 years to get into action and you will be writing your exam in 2013. So it would be better that if you are willing to take coaching for IIT-JEE you can take it, as the score of your entrance exam will anyway be counted. Otherwise if you feel so you can wait and complete your 12th boards with good score first and if by that time it gets implemented that fine and go in for a crash course only, and if not then take an year break to prepare for it.
Best of luck!