At a position of an Entry level Analyst,How would you approach an MD or CEO when you do not agree with the reforms they have put on your department?

I wouldn't.

1) You are not party to senior management information: there is a lot you don't know. 

2) You have no idea about the politics involved, which is most likely the most important factor

3) It is likely that your ideas, if they are good, have already been considered and rejected

4) The decisions have already been made - you are too late

5) If you are wrong, your advice is useless.  If you are right, you are telling your MD that she/he is stupid.  Is that really what you want to do?

6) Even if you are right, nobody cares what you think

Sorry to be so blunt!

Focus on making the reforms a success (failed reforms benefit nobody) and use your creativity to do better in your own job.

There is a prayer, goes something like this ....

"Grant me the patience to accept the things I cannot change, the strength to change the things I can, and the wisdom to know the difference"

Welcome to the management of the management of others and gradually imposes your management degree degree is an experience to enter the change in the process of business and how to behave correctly to get out of the situation,