Thing about Iran's governmental system, he may be the President but he is not the ultimate authority. The highest state official in Iran is the Supreme Leader.
The Supreme Leader:- Appoint non-governmental directors, foundations and tv/radio directors
- Position Currently filled by Ali Khammenei
- Intended to be an ayatollah (religious figure similar to Pope) of the entire community
- Appointed for Life
- Interpret the meaning of the Shari'a
- Eliminate Political Candidates
- Dismiss the President
- Command armed forces
- Nominate 6 members to the Guardian Council
- Appoints bonyads
Opposed to the President, Mahmoud Ahmadinejad:- Cheif Executive
- Second highest state official after Supreme Leader
- Devise Budget
- Supervise Economy
- Propose legislation
- Sign treaties, laws and agreements
- Chairs National Security Council
- Select VP and Cabinet
Basically the President has to fall in line with what the Supreme Leader wants done. So if we were to assassinate any official from Iran, it would be the Supreme Leader. However the Assembly of Religious Councils (86 members) would just appoint a new Shi'ite Supreme Leader.
So killing any one individual really won't change anything with Iran. Truth be told many citizens of Iran are not as extreme as their government, many have talked about hoping to start a revolution in Iran, however that is easier said than done.